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Crystal Structure of cytidine monophosphate hydroxymethylase MilA with hmCMP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5JNH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 8.5 289 0.1 M sodium cacodylate trihydrate(pH 6.5), 1.4 M sodium acetate trihydrate
Crystal Properties Matthews coefficient Solvent content 2.67 53.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 109.323 α = 90 b = 109.323 β = 90 c = 112.867 γ = 120
Symmetry Space Group P 32 2 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 ADSC QUANTUM 315r 2014-12-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 0.97912 SSRF BL17U
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 1.8 50 100 19.6 11.2 68810
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.86
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 5JNH 1.8 49.24 68810 3515 99.88 0.1881 0.1872 0.1944 0.2075 0.2117 RANDOM 22.571
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] -0.1 -0.1 -0.1 0.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.368 r_dihedral_angle_4_deg 13.717 r_dihedral_angle_3_deg 11.636 r_dihedral_angle_1_deg 5.085 r_mcangle_it 1.036 r_angle_refined_deg 0.984 r_angle_other_deg 0.698 r_mcbond_it 0.603 r_mcbond_other 0.603 r_chiral_restr 0.055
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.368 r_dihedral_angle_4_deg 13.717 r_dihedral_angle_3_deg 11.636 r_dihedral_angle_1_deg 5.085 r_mcangle_it 1.036 r_angle_refined_deg 0.984 r_angle_other_deg 0.698 r_mcbond_it 0.603 r_mcbond_other 0.603 r_chiral_restr 0.055 r_bond_refined_d 0.005 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5089 Nucleic Acid Atoms Solvent Atoms 201 Heterogen Atoms 46
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-3000 data scaling PHASER phasing