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Crystal structure of the reduced form of cytochrome c" from Methylophilus methylotrophus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other OXIDIZED STRUCTURE OF CYTOCHROME C""
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7 pH 7.00
Crystal Properties Matthews coefficient Solvent content 2.56 51.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.688 α = 90 b = 74.362 β = 90 c = 77.842 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 110 CCD MARRESEARCH 2002-10-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X11 EMBL/DESY, HAMBURG X11
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 1.94 46.86 97.9 0.083 7.2 4 25348 2
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 1.94 2.05 87.8 0.48 2.1 3.5
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 OXIDIZED STRUCTURE OF CYTOCHROME C" 1.95 25 23808 1283 98.5 0.188 0.185 0.1946 0.243 0.2503 RANDOM 25.35
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] -0.29 0.53 -0.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.813 r_scangle_it 5.503 r_scbond_it 3.455 r_mcangle_it 2.026 r_angle_other_deg 1.852 r_mcbond_it 1.12 r_nbd_refined 0.286 r_xyhbond_nbd_refined 0.204 r_symmetry_vdw_refined 0.19 r_symmetry_hbond_refined 0.165
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.813 r_scangle_it 5.503 r_scbond_it 3.455 r_mcangle_it 2.026 r_angle_other_deg 1.852 r_mcbond_it 1.12 r_nbd_refined 0.286 r_xyhbond_nbd_refined 0.204 r_symmetry_vdw_refined 0.19 r_symmetry_hbond_refined 0.165 r_chiral_restr 0.136 r_bond_refined_d 0.022 r_gen_planes_refined 0.01 r_bond_other_d r_angle_refined_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_gen_planes_other r_nbd_other r_nbtor_refined 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_mcangle_other r_scbond_other 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 1920 Nucleic Acid Atoms Solvent Atoms 270 Heterogen Atoms 146
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing