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Structure of Rolling Circle Replication Initiator Protein (RepDE) from Staphylococcus aureus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4CIJ PDB ENTRY 4CIJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8.5 0.5 M AMMONIUM CITRATE/AMMONIUM HYDROXIDE PH 8.5, 15% (W/V) PEG 8000
Crystal Properties Matthews coefficient Solvent content 3.04 59.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 240.3 α = 90 b = 56.536 β = 102.22 c = 62.357 γ = 90
Symmetry Space Group C 1 2 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 CCD ADSC Q4 MIRRORS 2008-08-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 Diamond I02
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 2.9 49.94 96.4 0.13 9.3 3.5 17447 -3
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 2.9 3.06 100 0.59 1.5 3.6
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 4CIJ 2.9 49.99 17447 939 99.5 0.21858 0.2163 0.2214 0.25894 0.264 RANDOM 83.095
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] -0.85 -0.83 -1.03 1.88
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.5 r_dihedral_angle_4_deg 23.495 r_dihedral_angle_3_deg 18.732 r_scangle_it 10.475 r_mcangle_it 8.925 r_dihedral_angle_1_deg 6.893 r_scbond_it 6.582 r_mcbond_it 5.666 r_mcbond_other 5.663 r_angle_refined_deg 1.504
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.5 r_dihedral_angle_4_deg 23.495 r_dihedral_angle_3_deg 18.732 r_scangle_it 10.475 r_mcangle_it 8.925 r_dihedral_angle_1_deg 6.893 r_scbond_it 6.582 r_mcbond_it 5.666 r_mcbond_other 5.663 r_angle_refined_deg 1.504 r_angle_other_deg 1.044 r_chiral_restr 0.086 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d 0.004 r_gen_planes_other 0.004 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4600 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing