2GTF

Crystal structure of nitrophorin 2 complex with pyrimidine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1PEEPDB ENTRY 1PEE

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.5298sodium citrate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
1.8834.62

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 34.374α = 90
b = 34.374β = 90
c = 255.82γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315bent Si-mirror2005-11-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 14-BM-C0.9APS14-BM-C

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.423.4910.08325290022900216
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.41.45730.68244255

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISTHROUGHOUTPDB ENTRY 1PEE1.423.42753027530147290.980.17140.17140.169340.21058RANDOM14.402
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]
-0.4-0.40.8
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.126
r_dihedral_angle_3_deg14.189
r_sphericity_free10.185
r_dihedral_angle_1_deg7.189
r_scangle_it4.814
r_sphericity_bonded4.285
r_scbond_it3.797
r_mcangle_it2.927
r_mcbond_it2.342
r_rigid_bond_restr2.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.126
r_dihedral_angle_3_deg14.189
r_sphericity_free10.185
r_dihedral_angle_1_deg7.189
r_scangle_it4.814
r_sphericity_bonded4.285
r_scbond_it3.797
r_mcangle_it2.927
r_mcbond_it2.342
r_rigid_bond_restr2.002
r_angle_refined_deg1.895
r_dihedral_angle_4_deg1.608
r_angle_other_deg1.527
r_mcbond_other0.847
r_nbd_refined0.208
r_symmetry_vdw_other0.205
r_nbd_other0.197
r_symmetry_hbond_refined0.193
r_nbtor_refined0.183
r_xyhbond_nbd_refined0.167
r_symmetry_vdw_refined0.166
r_chiral_restr0.118
r_nbtor_other0.093
r_bond_refined_d0.021
r_gen_planes_refined0.01
r_bond_other_d0.004
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1442
Nucleic Acid Atoms
Solvent Atoms160
Heterogen Atoms49

Software

Software
Software NamePurpose
REFMACrefinement
XDISPLAYFdata reduction
HKL-2000data scaling