1RL4
Plasmodium falciparum peptide deformylase complex with inhibitor
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 1JYM | PDB ENTRY 1JYM |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 6.1 | 294 | sodium monobasic phosphate, potassium dibasic phosphate, lithium sulfate, CAPS, pH 6.1, VAPOR DIFFUSION, SITTING DROP, temperature 294K |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
4.01 | 69.35 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 102.317 | α = 90 |
b = 102.317 | β = 90 |
c = 118.339 | γ = 120 |
Symmetry | |
---|---|
Space Group | P 65 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | CCD | ADSC QUANTUM 4 | 2002-03-17 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ALS BEAMLINE 5.0.2 | 0.98 | ALS | 5.0.2 |
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 | 2.18 | 41.6 | 99.9 | 0.111 | 11.4 | 6.3 | 36742 | -3 | 33.9 |
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 | 2.18 | 2.3 | 100 | 0.714 | 2.6 | 6.3 | 5325 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Factor (Observed) | R-Work (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | R-Free Selection Details | Mean Isotropic B | ||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 1JYM | 2.18 | 20 | 36594 | 36594 | 1811 | 99.99 | 0.19806 | 0.19806 | 0.1973 | 0.21 | 0.2122 | 0.23 | RANDOM | 39.587 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_scangle_it | 8.397 |
r_dihedral_angle_1_deg | 5.872 |
r_scbond_it | 5.727 |
r_mcangle_it | 4.314 |
r_mcbond_it | 2.442 |
r_angle_refined_deg | 1.313 |
r_symmetry_hbond_refined | 0.304 |
r_nbd_refined | 0.23 |
r_xyhbond_nbd_refined | 0.219 |
r_symmetry_vdw_refined | 0.185 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 2555 |
Nucleic Acid Atoms | |
Solvent Atoms | 139 |
Heterogen Atoms | 128 |
Software
Software | |
---|---|
Software Name | Purpose |
REFMAC | refinement |
MOSFLM | data reduction |
CCP4 | data scaling |
MOLREP | phasing |