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Crystal structure of mMsoI/DNA complex with calcium
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1M5X
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.3 291 22% PEG 400, 100 mM Tris pH 7.3, 10 mM calcium chloride, 20 mM sodium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 1.93 36.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.932 α = 107.21 b = 41.933 β = 95.43 c = 70.96 γ = 109.44
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray IMAGE PLATE RIGAKU RAXIS IV 2008-03-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE OTHER
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 2.69 50 97 0.052 21 3.9 11073
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 2.69 2.8 95.8 0.258 4.51 3.9
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 1M5X 2.69 50 10862 546 96.6 0.215 0.211 0.2119 0.281 0.2721 RANDOM 59.2
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] 2.72 4.6 -6.76 1.75 -3.57 0.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.787 r_dihedral_angle_1_deg 5.122 r_angle_refined_deg 1.11 r_nbtor_refined 0.304 r_nbd_refined 0.198 r_xyhbond_nbd_refined 0.142 r_chiral_restr 0.064 r_bond_refined_d 0.008 r_gen_planes_refined 0.003 r_bond_other_d
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.787 r_dihedral_angle_1_deg 5.122 r_angle_refined_deg 1.11 r_nbtor_refined 0.304 r_nbd_refined 0.198 r_xyhbond_nbd_refined 0.142 r_chiral_restr 0.064 r_bond_refined_d 0.008 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_gen_planes_other r_nbd_other r_nbtor_other 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_it r_mcbond_other r_mcangle_it r_scbond_it r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2720 Nucleic Acid Atoms 978 Solvent Atoms 35 Heterogen Atoms 2
Software Software Software Name Purpose HKL-2000 data collection PHASES phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling