2EVR | pdb_00002evr

CRYSTAL STRUCTURE OF A PUTATIVE GAMMA-D-GLUTAMYL-L-DIAMINO ACID ENDOPEPTIDASE (NPUN_R0659) FROM NOSTOC PUNCTIFORME PCC 73102 AT 1.60 A RESOLUTION


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP, NANODROP2772.0M NaCl, 10.0% PEG-6000, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
3.1961.16

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 90.47α = 90
b = 90.47β = 90
c = 93.81γ = 90
Symmetry
Space GroupP 41 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102005-09-28MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.2.11.0163, 0.9797ALS8.2.1

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
11.628.71970.1159.364.3151615
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)
11.61.6690900.8212.153.33

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)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMADTHROUGHOUT1.628.7148970262499.410.160.1590.170.1760.19RANDOM20.031
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]
-0.12-0.120.24
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.234
r_dihedral_angle_4_deg15.317
r_dihedral_angle_3_deg11.752
r_scangle_it6.192
r_dihedral_angle_1_deg5.766
r_scbond_it4.409
r_mcangle_it3.153
r_mcbond_it1.817
r_angle_refined_deg1.508
r_angle_other_deg0.818
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.234
r_dihedral_angle_4_deg15.317
r_dihedral_angle_3_deg11.752
r_scangle_it6.192
r_dihedral_angle_1_deg5.766
r_scbond_it4.409
r_mcangle_it3.153
r_mcbond_it1.817
r_angle_refined_deg1.508
r_angle_other_deg0.818
r_mcbond_other0.498
r_symmetry_vdw_refined0.267
r_symmetry_vdw_other0.241
r_metal_ion_refined0.231
r_nbd_refined0.219
r_nbtor_refined0.189
r_symmetry_hbond_refined0.189
r_xyhbond_nbd_refined0.182
r_nbd_other0.18
r_chiral_restr0.097
r_nbtor_other0.09
r_bond_refined_d0.016
r_gen_planes_refined0.008
r_gen_planes_other0.003
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1714
Nucleic Acid Atoms
Solvent Atoms290
Heterogen Atoms22

Software

Software
Software NamePurpose
REFMACrefinement
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing