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CYTOCHROME C PRIME FROM ALCALIGENES XYLOSOXIDANS: CARBON MONOOXIDE BOUND L16A VARIANT AT 1.03 A RESOLUTION - Restraint refinement
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2YL0 PDB ENTRY 2YL0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 AMMONIUM SULPHATE, TRIS PH 7.5
Crystal Properties Matthews coefficient Solvent content 2.74 55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.009 α = 90 b = 53.009 β = 90 c = 181.114 γ = 120
Symmetry Space Group P 65 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M MIRRORS 2009-06-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA SLS X06SA
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 1.03 36.54 100 0.07 12.7 7.8 75580 11.8
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 1.03 1.09 99.9 0.71 2.5 6.4
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 2YL0 1.03 32.24 71654 3799 99.94 0.13386 0.13339 0.133 0.14271 0.1425 RANDOM 13.975
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] 0.35 0.17 0.35 -0.52
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.993 r_dihedral_angle_4_deg 19.083 r_dihedral_angle_3_deg 15.635 r_dihedral_angle_1_deg 5.464 r_scangle_it 5.439 r_scbond_it 3.774 r_mcangle_it 2.915 r_angle_other_deg 2.362 r_angle_refined_deg 1.935 r_mcbond_it 1.842
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.993 r_dihedral_angle_4_deg 19.083 r_dihedral_angle_3_deg 15.635 r_dihedral_angle_1_deg 5.464 r_scangle_it 5.439 r_scbond_it 3.774 r_mcangle_it 2.915 r_angle_other_deg 2.362 r_angle_refined_deg 1.935 r_mcbond_it 1.842 r_rigid_bond_restr 1.489 r_mcbond_other 0.522 r_chiral_restr 0.114 r_bond_refined_d 0.018 r_gen_planes_refined 0.013 r_gen_planes_other 0.005 r_bond_other_d 0.002 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_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 946 Nucleic Acid Atoms Solvent Atoms 280 Heterogen Atoms 45
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing