2IZZ

Crystal structure of human pyrroline-5-carboxylate reductase


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2AG8PDB ENTRY 2AG8

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.520% PEG3350, 10% ETHYLENE GLYCOL 0.2M NA2SO4, 0.1M BIS-TRIS PROPANE PH7.5, pH 7.50
Crystal Properties
Matthews coefficientSolvent content
2.4349.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 110.453α = 90
b = 177.944β = 106.7
c = 87.916γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2006-06-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SASLSX10SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
11.954099.90.0611.93.111774425.5
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.952.0699.90.382.32.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2AG81.9540115902183599.90.1670.1660.19RANDOM23.71
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]
0.790.281.6-2.23
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.597
r_dihedral_angle_4_deg13.197
r_dihedral_angle_3_deg12.712
r_dihedral_angle_1_deg5.685
r_scangle_it2.249
r_angle_other_deg1.497
r_angle_refined_deg1.455
r_scbond_it1.404
r_mcangle_it0.921
r_mcbond_it0.556
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.597
r_dihedral_angle_4_deg13.197
r_dihedral_angle_3_deg12.712
r_dihedral_angle_1_deg5.685
r_scangle_it2.249
r_angle_other_deg1.497
r_angle_refined_deg1.455
r_scbond_it1.404
r_mcangle_it0.921
r_mcbond_it0.556
r_symmetry_vdw_other0.213
r_nbd_refined0.199
r_nbd_other0.186
r_symmetry_vdw_refined0.176
r_nbtor_refined0.16
r_chiral_restr0.146
r_symmetry_hbond_refined0.13
r_xyhbond_nbd_refined0.128
r_nbtor_other0.087
r_bond_refined_d0.011
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9935
Nucleic Acid Atoms
Solvent Atoms695
Heterogen Atoms248

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing