3BE7

Crystal structure of Zn-dependent arginine carboxypeptidase


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2R8CPDB ENTRY 2R8C

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17294100mM Succinic acid pH 7.0, 15% PEG 3350, 10% Glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Crystal Properties
Matthews coefficientSolvent content
2.9858.73

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 113.42α = 90
b = 146.583β = 90
c = 255.963γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315MIRRORS2007-06-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X29ANSLSX29A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
12.155094.80.130.13.74.2230541-0.520.2
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.152.2387.40.520.540.82.7

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 2R8C2.320175832545195.960.227670.226020.27981RANDOM48.347
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]
-1.441.48-0.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.46
r_dihedral_angle_3_deg21.232
r_dihedral_angle_4_deg14.081
r_scangle_it13.485
r_scbond_it10.02
r_dihedral_angle_1_deg9.968
r_mcangle_it7.128
r_mcbond_it5.189
r_angle_refined_deg1.05
r_nbtor_refined0.29
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.46
r_dihedral_angle_3_deg21.232
r_dihedral_angle_4_deg14.081
r_scangle_it13.485
r_scbond_it10.02
r_dihedral_angle_1_deg9.968
r_mcangle_it7.128
r_mcbond_it5.189
r_angle_refined_deg1.05
r_nbtor_refined0.29
r_xyhbond_nbd_refined0.149
r_nbd_refined0.127
r_symmetry_hbond_refined0.106
r_chiral_restr0.104
r_symmetry_vdw_refined0.089
r_bond_refined_d0.006
r_gen_planes_refined0.003
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_other
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 Atoms24048
Nucleic Acid Atoms
Solvent Atoms572
Heterogen Atoms194

Software

Software
Software NamePurpose
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling