1BSZ
PEPTIDE DEFORMYLASE AS FE2+ CONTAINING FORM (NATIVE) IN COMPLEX WITH INHIBITOR POLYETHYLENE GLYCOL
X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 1ICJ | |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | 7.4 | SEE: D.GROCHE,A.BECKER,I.SCHLICHTING,W.KABSCH, S.SCHULTZ,A.F.V.WAGNER (1998) BIOCHEM.BIOPHYS.RES.COMM. 246, 342, pH 7.4 | ||
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.89 | 57 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 141 | α = 90 |
| b = 63.4 | β = 120.6 |
| c = 86.8 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | C 1 2 1 |
Diffraction
| Diffraction Experiment | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
| 1 | 1 | x-ray | 293 | AREA DETECTOR | SIEMENS-NICOLET X100 | FRANKS DOUBLE-MIRROR | 1997-03-15 | M | SINGLE WAVELENGTH | |||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | ROTATING ANODE | ELLIOTT GX-18 | |||
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Sym I (Observed) | Net I Over Average Sigma (I) | Redundancy | Number Reflections (All) | Number Reflections (Observed) | Observed Criterion Sigma (F) | Observed Criterion Sigma (I) | B (Isotropic) From Wilson Plot | ||||||||
| 1 | 1.9 | 20 | 96.1 | 0.059 | 9.99 | 2.1 | 50232 | 20.3 | |||||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
| 1 | 1.9 | 2.01 | 92.8 | 0.296 | 1.51 | 1.8 | |||||||||||||
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 1ICJ | 1.9 | 6 | 46155 | 4711 | 96.7 | 0.197 | 0.197 | 0.247 | RANDOM | 29.8 | ||||||
| Temperature Factor Modeling | ||||||
|---|---|---|---|---|---|---|
| Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| x_dihedral_angle_d | 25.4 |
| x_scangle_it | 3.71 |
| x_scbond_it | 2.26 |
| x_improper_angle_d | 2.08 |
| x_mcangle_it | 1.9 |
| x_angle_deg | 1.2 |
| x_mcbond_it | 1.16 |
| x_bond_d | 0.011 |
| x_bond_d_na | |
| x_bond_d_prot | |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 4038 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 211 |
| Heterogen Atoms | 97 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| X-PLOR | model building |
| X-PLOR | refinement |
| XDS | data reduction |
| XSCALE | data scaling |
| X-PLOR | phasing |
