2ZLB

Crystal structure of APO form of rat catechol-O-methyltransferase


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1VIDPDB entry 1VID

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.52930.2M (NH4)2SO4, 30% PEG 8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.1542.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 56.262α = 90
b = 56.262β = 90
c = 117.483γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray93CCDRIGAKU JUPITER 2102003-07-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL32B21.0SPring-8BL32B2

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
12.239.1698.70.07207.21135634.11
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)
2.22.3294.60.2417.57.11565

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 1VID2.2151073553598.570.1980.181590.178770.23747RANDOM25.767
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]
-0.66-0.33-0.660.99
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.751
r_dihedral_angle_3_deg20.761
r_dihedral_angle_4_deg16.708
r_dihedral_angle_1_deg10.114
r_scangle_it4.309
r_scbond_it2.8
r_angle_refined_deg2.144
r_mcangle_it2.052
r_mcbond_it1.292
r_nbtor_refined0.32
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.751
r_dihedral_angle_3_deg20.761
r_dihedral_angle_4_deg16.708
r_dihedral_angle_1_deg10.114
r_scangle_it4.309
r_scbond_it2.8
r_angle_refined_deg2.144
r_mcangle_it2.052
r_mcbond_it1.292
r_nbtor_refined0.32
r_xyhbond_nbd_refined0.28
r_nbd_refined0.252
r_symmetry_vdw_refined0.187
r_symmetry_hbond_refined0.187
r_chiral_restr0.159
r_bond_refined_d0.02
r_gen_planes_refined0.008
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 Atoms1672
Nucleic Acid Atoms
Solvent Atoms149
Heterogen Atoms5

Software

Software
Software NamePurpose
REFMACrefinement
BSSdata collection
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing