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Structural and functional studies the characterization of Cys4 Zinc-finger motif in the recombination mediator protein RecR
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3VDP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.4 293 8%(W/V) PEG3350, 200MM LITHIUM CITRIC TRIBASIC TETRAHYDRATE, 100MM MES, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.07 59.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.604 α = 90 b = 67.912 β = 92.98 c = 94.364 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 0.9875 Photon Factory BL-17A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.7 20 21645
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 3VDP 3 20 21645 1156 98.5 0.222 0.22 0.2273 0.255 0.2407 RANDOM 76.9
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] -3.24 2.45 6.72 -3.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.666 r_dihedral_angle_3_deg 22.118 r_dihedral_angle_4_deg 20.088 r_scangle_it 9.35 r_dihedral_angle_1_deg 7.275 r_mcangle_it 7.151 r_scbond_it 5.185 r_mcbond_it 3.945 r_rigid_bond_restr 3.301 r_angle_refined_deg 1.946
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.666 r_dihedral_angle_3_deg 22.118 r_dihedral_angle_4_deg 20.088 r_scangle_it 9.35 r_dihedral_angle_1_deg 7.275 r_mcangle_it 7.151 r_scbond_it 5.185 r_mcbond_it 3.945 r_rigid_bond_restr 3.301 r_angle_refined_deg 1.946 r_chiral_restr 0.115 r_bond_refined_d 0.019 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6058 Nucleic Acid Atoms Solvent Atoms 132 Heterogen Atoms 19
Software Software Software Name Purpose PHASES phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling