1ZRS

wild-type LD-carboxypeptidase


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.5294citric acid, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Crystal Properties
Matthews coefficientSolvent content
1.9837

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 52.185α = 90
b = 78.271β = 104.33
c = 71.258γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2004-11-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONMPG/DESY, HAMBURG BEAMLINE BW61.05MPG/DESY, HAMBURGBW6

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
11.52097.10.0370.03720.92.2862248622416
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)
11.51.5295.10.2520.252423359

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONMIRASTHROUGHOUT1.5208189981899432597.180.164420.164420.163730.1773RANDOM13.085
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]
1.980.37-0.65-1.14
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.72
r_scangle_it4.194
r_scbond_it2.508
r_mcangle_it1.55
r_angle_refined_deg1.46
r_mcbond_it0.863
r_angle_other_deg0.843
r_symmetry_vdw_other0.333
r_nbd_other0.255
r_symmetry_vdw_refined0.233
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.72
r_scangle_it4.194
r_scbond_it2.508
r_mcangle_it1.55
r_angle_refined_deg1.46
r_mcbond_it0.863
r_angle_other_deg0.843
r_symmetry_vdw_other0.333
r_nbd_other0.255
r_symmetry_vdw_refined0.233
r_nbd_refined0.223
r_xyhbond_nbd_refined0.126
r_chiral_restr0.092
r_nbtor_other0.082
r_symmetry_hbond_refined0.058
r_gen_planes_other0.015
r_bond_refined_d0.013
r_gen_planes_refined0.009
r_bond_other_d0.007
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_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 Atoms4505
Nucleic Acid Atoms
Solvent Atoms313
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing