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Restriction endonuclease MvaI-cognate DNA substrate complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2OA9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.9 294 0.1 M HEPES pH 7.89, 0.2 M CaCl2, 25 % PEG4000, pH 7.9, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 2.19 43.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.848 α = 90 b = 81.38 β = 90.52 c = 71.308 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 100 CCD MARRESEARCH BENT MIRROR 2006-09-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MPG/DESY, HAMBURG BEAMLINE BW6 1.05 MPG/DESY, HAMBURG BW6
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 1.5 30 96.6 0.07 6.2 3.1 94979 94979 14.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.58 95.3 0.29 2.5 3.1 13630
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 2OA9 1.5 30 94977 94977 4789 97.65 0.177 0.177 0.176 0.1761 0.194 0.1932 THIN RESOLUTION SHELLS 11.782
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] -0.56 -0.03 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.883 r_dihedral_angle_4_deg 15.227 r_dihedral_angle_3_deg 12.533 r_dihedral_angle_1_deg 5.853 r_scangle_it 2.403 r_scbond_it 1.729 r_angle_refined_deg 1.189 r_mcangle_it 1.118 r_mcbond_it 0.794 r_nbtor_refined 0.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.883 r_dihedral_angle_4_deg 15.227 r_dihedral_angle_3_deg 12.533 r_dihedral_angle_1_deg 5.853 r_scangle_it 2.403 r_scbond_it 1.729 r_angle_refined_deg 1.189 r_mcangle_it 1.118 r_mcbond_it 0.794 r_nbtor_refined 0.303 r_nbd_refined 0.192 r_symmetry_vdw_refined 0.172 r_symmetry_hbond_refined 0.151 r_xyhbond_nbd_refined 0.111 r_metal_ion_refined 0.109 r_chiral_restr 0.074 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4013 Nucleic Acid Atoms 868 Solvent Atoms 576 Heterogen Atoms 7
Software Software Software Name Purpose REFMAC refinement MAR345 data collection MOSFLM data reduction CCP4 data scaling MOLREP phasing NCSREF phasing