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The crystal structure of MPP8
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3DM1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.5 25%PEG400, 0.2M MgCl2, 0.1M Hepes 7.5, VAPOR DIFFUSION
Crystal Properties Matthews coefficient Solvent content 3.12 60.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.665 α = 90 b = 50.665 β = 90 c = 123.538 γ = 120
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 QUANTUM 315 2009-12-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.9794 APS 19-ID
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 2.05 50 99.7 0.076 8.4 11.3 11280
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 2.05 2.09 99.6 0.853 11.2 551
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 3DM1 2.05 43.88 11249 537 99.88 0.22 0.217 0.2151 0.283 0.275 RANDOM 36.832
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] 0.58 0.29 0.58 -0.87
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.989 r_dihedral_angle_4_deg 26.161 r_dihedral_angle_3_deg 17.171 r_dihedral_angle_1_deg 6.391 r_scangle_it 5.286 r_scbond_it 3.172 r_mcangle_it 2.021 r_angle_refined_deg 1.563 r_mcbond_it 1.115 r_chiral_restr 0.113
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.989 r_dihedral_angle_4_deg 26.161 r_dihedral_angle_3_deg 17.171 r_dihedral_angle_1_deg 6.391 r_scangle_it 5.286 r_scbond_it 3.172 r_mcangle_it 2.021 r_angle_refined_deg 1.563 r_mcbond_it 1.115 r_chiral_restr 0.113 r_bond_refined_d 0.018 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 986 Nucleic Acid Atoms Solvent Atoms 67 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction HKL-3000 data reduction