6VJ6 | pdb_00006vj6

2.55 Angstrom Resolution Crystal Structure of Peptidylprolyl Isomerase (PrsA) from Bacillus cereus


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7292Protein: 8.3 mg/ml, 0.01M Tris pH 8.3; Reservior (Screen JCSG+, G1): 0.1M HEPES pH 7.0, 30% v/v Jeffamine ED-2001 pH 7.0
Crystal Properties
Matthews coefficientSolvent content
3.666.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 151.425α = 90
b = 70.358β = 91.749
c = 79.357γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDC(111)2019-11-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-G0.97856APS21-ID-G

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym I (Observed)Rrim I (All)Rpim I (All)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
12.553099.90.0840.0840.0950.04418.1527237-356.3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.552.591000.7870.7870.8830.3940.8312.35.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)Mean Isotropic B
X-RAY DIFFRACTIONSADFREE R-VALUE2.55329.7327229138299.6450.2190.21740.220.24740.2577.617
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]
-5.799-1.495-7.0512.917
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg19.598
r_lrange_it10.751
r_lrange_other10.748
r_dihedral_angle_3_deg8.763
r_dihedral_angle_4_deg8.272
r_scangle_it7.583
r_scangle_other7.582
r_mcangle_it6.322
r_mcangle_other6.321
r_scbond_it4.761
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg19.598
r_lrange_it10.751
r_lrange_other10.748
r_dihedral_angle_3_deg8.763
r_dihedral_angle_4_deg8.272
r_scangle_it7.583
r_scangle_other7.582
r_mcangle_it6.322
r_mcangle_other6.321
r_scbond_it4.761
r_scbond_other4.76
r_mcbond_it4.163
r_mcbond_other4.163
r_dihedral_angle_1_deg1.828
r_angle_refined_deg1.452
r_angle_other_deg0.384
r_nbd_refined0.219
r_symmetry_xyhbond_nbd_refined0.204
r_nbd_other0.185
r_symmetry_nbd_other0.174
r_nbtor_refined0.169
r_xyhbond_nbd_refined0.163
r_symmetry_nbd_refined0.151
r_ncsr_local_group_10.123
r_symmetry_nbtor_other0.092
r_chiral_restr0.07
r_gen_planes_refined0.054
r_gen_planes_other0.054
r_bond_refined_d0.005
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4180
Nucleic Acid Atoms
Solvent Atoms157
Heterogen Atoms50

Software

Software
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing