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CcpA from G. sulfurreducens, S134P variant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3HQ6 PDB ENTRY 3HQ6
Crystallization Crystal Properties Matthews coefficient Solvent content 2.31 46.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.899 α = 104.71 b = 55.473 β = 99.39 c = 68.606 γ = 108.97
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray CCD MAR CCD 165 mm 2009-03-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X12 1.05 EMBL/DESY, HAMBURG X12
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.52 90 90.1 0.053 18 1.9 86506
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 3HQ6 1.52 63.92 86506 4560 90.14 0.16135 0.16018 0.1659 0.18379 0.185 RANDOM 14.95
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] -0.11 0.54 -0.69 0.7 0.61 -0.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.641 r_dihedral_angle_4_deg 19.104 r_dihedral_angle_3_deg 12.902 r_dihedral_angle_1_deg 5.626 r_scangle_it 2.767 r_scbond_it 1.746 r_angle_refined_deg 1.208 r_mcangle_it 1.093 r_angle_other_deg 0.869 r_mcbond_it 0.603
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.641 r_dihedral_angle_4_deg 19.104 r_dihedral_angle_3_deg 12.902 r_dihedral_angle_1_deg 5.626 r_scangle_it 2.767 r_scbond_it 1.746 r_angle_refined_deg 1.208 r_mcangle_it 1.093 r_angle_other_deg 0.869 r_mcbond_it 0.603 r_mcbond_other 0.153 r_chiral_restr 0.068 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4651 Nucleic Acid Atoms Solvent Atoms 541 Heterogen Atoms 230
Software Software Software Name Purpose REFMAC refinement