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Crystal Structure of Vibrio salmonicida catalase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1M85 PDB ENTRY 1m85 mutated to fit the Vibrio salmonicida catalase sequence
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 2.0M Ammonium sulphate, 2% PEG400, 100mM Na-Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.26 45.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.15 α = 90 b = 217.76 β = 110.48 c = 99.28 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE MAR scanner 345 mm plate mirrors 2005-07-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM1A 0.874 ESRF BM1A
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) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.96 20.089 0.111 0.111 6 2.6 700270 267579 16.8
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) 1 1.96 2.06 0.361 2 2.5 267579
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 1m85 mutated to fit the Vibrio salmonicida catalase sequence 1.97 20 267579 252769 13408 96.5 0.15082 0.14818 0.1478 0.20034 0.2006 RANDOM 14.011
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] -1.17 -0.32 0.74 0.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.574 r_dihedral_angle_4_deg 16.542 r_dihedral_angle_3_deg 14.215 r_dihedral_angle_1_deg 6.093 r_scangle_it 2.035 r_scbond_it 1.383 r_angle_refined_deg 1.268 r_mcangle_it 0.792 r_mcbond_it 0.488 r_nbtor_refined 0.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.574 r_dihedral_angle_4_deg 16.542 r_dihedral_angle_3_deg 14.215 r_dihedral_angle_1_deg 6.093 r_scangle_it 2.035 r_scbond_it 1.383 r_angle_refined_deg 1.268 r_mcangle_it 0.792 r_mcbond_it 0.488 r_nbtor_refined 0.303 r_symmetry_vdw_refined 0.195 r_nbd_refined 0.193 r_symmetry_hbond_refined 0.162 r_xyhbond_nbd_refined 0.14 r_metal_ion_refined 0.1 r_chiral_restr 0.096 r_bond_refined_d 0.01 r_gen_planes_refined 0.004 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_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 30920 Nucleic Acid Atoms Solvent Atoms 4594 Heterogen Atoms 396
Software Software Software Name Purpose REFMAC refinement MAR345 data collection XDS data reduction CCP4 data scaling PHASER phasing