2AMF

Crystal structure of 1-Pyrroline-5-Carboxylate Reductase from Human Pathogen Streptococcus Pyogenes


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2AHRpdb entry 2AHR

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP72983.5 M sodium formate, pH 7.0, temperature 298K, VAPOR DIFFUSION, HANGING DROP
Crystal Properties
Matthews coefficientSolvent content
2.8857

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 171.822α = 90
b = 109.96β = 95.38
c = 84.158γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 4mirrors2005-04-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.9795APS19-ID

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
12.25098.50.061801257892322
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)
12.22.2892.50.326

Refinement

Statistics
Diffraction IDStructure Solution 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 DIFFRACTIONisomorphous to 2AHRpdb entry 2AHR2.2507824674316393099.160.175490.175490.173330.21542RANDOM35.756
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]
2.20.25-0.43-1.73
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.76
r_dihedral_angle_4_deg19.112
r_dihedral_angle_3_deg16.936
r_dihedral_angle_1_deg5.702
r_scangle_it2.956
r_scbond_it1.799
r_angle_refined_deg1.329
r_mcangle_it0.953
r_mcbond_it0.501
r_nbtor_refined0.295
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.76
r_dihedral_angle_4_deg19.112
r_dihedral_angle_3_deg16.936
r_dihedral_angle_1_deg5.702
r_scangle_it2.956
r_scbond_it1.799
r_angle_refined_deg1.329
r_mcangle_it0.953
r_mcbond_it0.501
r_nbtor_refined0.295
r_nbd_refined0.204
r_xyhbond_nbd_refined0.152
r_chiral_restr0.087
r_bond_refined_d0.012
r_gen_planes_refined0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9619
Nucleic Acid Atoms
Solvent Atoms739
Heterogen Atoms85

Software

Software
Software NamePurpose
REFMACrefinement
SBC-Collectdata collection
HKL-2000data scaling