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Cytochrome b5 of Ostreococcus tauri virus 2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2IBJ PDB ENTRY 2IBJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 4.6 2 M AMMONIUM SULPHATE, 0.1 M SODIUM ACETATE PH 4.6
Crystal Properties Matthews coefficient Solvent content 2.04 39.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.69 α = 90 b = 58.5 β = 90 c = 127.07 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 ADSC CCD 2010-05-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 Diamond I03
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 1.95 45.7 99.7 0.13 8.2 5.7 25529
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 1.95 2.06 100 0.9 2 5.8
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 2IBJ 1.95 63.54 24163 1315 99.52 0.19101 0.18768 0.1878 0.25368 0.2539 RANDOM 34.881
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] -0.8 0.1 0.7
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.307 r_dihedral_angle_3_deg 15.473 r_dihedral_angle_4_deg 8.036 r_dihedral_angle_1_deg 5.847 r_angle_refined_deg 3.378 r_chiral_restr 0.083 r_gen_planes_refined 0.011 r_bond_refined_d 0.01 r_bond_other_d r_angle_other_deg
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.307 r_dihedral_angle_3_deg 15.473 r_dihedral_angle_4_deg 8.036 r_dihedral_angle_1_deg 5.847 r_angle_refined_deg 3.378 r_chiral_restr 0.083 r_gen_planes_refined 0.011 r_bond_refined_d 0.01 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2667 Nucleic Acid Atoms Solvent Atoms 199 Heterogen Atoms 192
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing