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Hexameric Replicative DNA Helicase RepA from Plasmid RSF1010 - Cubic Crystal Structure
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1G8Y PDB ENTRY 1G8Y
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 291 SITTING DROP VAPOR DIFFUSION AT 291K. PROTEIN STOCK: 26MG/ML REPA, 10MM TRIS-HCL PH8.0, 150MM NACL, 0.1MM EDTA. PRECIPITANT: 100MM TRIS-HCL PH 7.5, 26% PEG400, 100MM MGSO4
Crystal Properties Matthews coefficient Solvent content 4.8 74.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 190.293 α = 90 b = 190.293 β = 90 c = 190.293 γ = 90
Symmetry Space Group P 43 3 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 IMAGE PLATE MARRESEARCH MIRRORS 2000-12-15 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE ENRAF-NONIUS FR571
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 2.52 150 99.1 0.106 13.6 7.64 40046
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 2.52 2.58 89.7 0.6 3.3 4.1
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-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MAD THROUGHOUT PDB ENTRY 1G8Y 2.55 25 37753 991 99.8 0.176 0.1911 0.211 0.2232 RANDOM 34.09
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]
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 4.223 r_scbond_it 2.633 r_mcangle_it 1.564 r_mcbond_it 0.829 r_bond_refined_d r_bond_other_d r_angle_refined_deg r_angle_other_deg r_dihedral_angle_1_deg r_dihedral_angle_2_deg
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 4.223 r_scbond_it 2.633 r_mcangle_it 1.564 r_mcbond_it 0.829 r_bond_refined_d r_bond_other_d r_angle_refined_deg r_angle_other_deg r_dihedral_angle_1_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_chiral_restr r_gen_planes_refined r_gen_planes_other 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_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 3810 Nucleic Acid Atoms Solvent Atoms 421 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling