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Crystal structure of holo form of rat catechol-o-methyltransferase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1VID PDB entry 1vid
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 298 0.2M (NH4)2SO4, 26% PEG 8000, 0.2% Sucrose, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.13 42.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 32.903 α = 90 b = 61.089 β = 90 c = 105.369 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD RIGAKU JUPITER 210 2003-05-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL32B2 1.000 SPring-8 BL32B2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.6 52.85 100 0.101 14 6.8 6949 6906 1 1 45.1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.6 2.74 100 0.374 5.1 7.1 1000
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (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 Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 1vid 2.6 39.9 6225 688 99.37 0.19573 0.18692 0.1902 0.28053 0.2816 RANDOM 32.263
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] 2.88 -2.29 -0.59
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.161 r_dihedral_angle_4_deg 26.961 r_dihedral_angle_3_deg 21.487 r_dihedral_angle_1_deg 7.673 r_scangle_it 2.676 r_angle_refined_deg 2.002 r_scbond_it 1.733 r_mcangle_it 1.279 r_mcbond_it 0.72 r_nbtor_refined 0.315
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.161 r_dihedral_angle_4_deg 26.961 r_dihedral_angle_3_deg 21.487 r_dihedral_angle_1_deg 7.673 r_scangle_it 2.676 r_angle_refined_deg 2.002 r_scbond_it 1.733 r_mcangle_it 1.279 r_mcbond_it 0.72 r_nbtor_refined 0.315 r_symmetry_vdw_refined 0.262 r_nbd_refined 0.244 r_symmetry_hbond_refined 0.206 r_xyhbond_nbd_refined 0.18 r_chiral_restr 0.177 r_bond_refined_d 0.016 r_gen_planes_refined 0.006 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 Atoms Number Protein Atoms 1615 Nucleic Acid Atoms Solvent Atoms 42 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling AMoRE phasing