3DUG | pdb_00003dug

Crystal structure of zn-dependent arginine carboxypeptidase complexed with zinc


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3BE7PDB ENTRY 3BE7

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7294100MM SUCCINIC ACID PH 7.0, 15% PEG 3350, 5MM ZINC SULFATE, 10% GLYCEROL, VAPOR DIFFUSION, SITTING DROP, REMARK TEMPERATURE 294K, pH 7.00
Crystal Properties
Matthews coefficientSolvent content
2.9858.73

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 113.325α = 90
b = 146.04β = 90
c = 255.646γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315MIRRORS2007-09-21MSINGLE 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
12.625099.40.110.114.13.6127892-0.5
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)
12.622.7198.40.790.73

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 3BE72.6220122571380899.10.231060.230080.230.263640.27RANDOM75.913
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]
-3.53.310.19
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.96
r_dihedral_angle_3_deg17.842
r_dihedral_angle_4_deg14.334
r_scangle_it6.689
r_dihedral_angle_1_deg5.944
r_scbond_it4.099
r_mcangle_it3.682
r_mcbond_it2.259
r_angle_refined_deg1.175
r_nbtor_refined0.296
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.96
r_dihedral_angle_3_deg17.842
r_dihedral_angle_4_deg14.334
r_scangle_it6.689
r_dihedral_angle_1_deg5.944
r_scbond_it4.099
r_mcangle_it3.682
r_mcbond_it2.259
r_angle_refined_deg1.175
r_nbtor_refined0.296
r_symmetry_hbond_refined0.266
r_symmetry_vdw_refined0.191
r_xyhbond_nbd_refined0.16
r_nbd_refined0.141
r_chiral_restr0.08
r_bond_refined_d0.008
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 Atoms24026
Nucleic Acid Atoms
Solvent Atoms286
Heterogen Atoms188

Software

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