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Crystal structure of UMP kinase from Ureaplasma parvum
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2A1F PDB ENTRY 2A1F
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 0.2 M AMMONIUM FLUORIDE, 20% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.4 47.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.753 α = 90 b = 96.552 β = 105.75 c = 96.27 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 ADSC CCD TOROIDAL FOCUSING MIRROR M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 ESRF ID14-4
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 2.5 33.42 99.9 0.12 11.4 3.8 48558 2
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 2.5 2.64 99.9 0.12 3.1 3.6
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-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2A1F 2.5 20 46149 2456 99.9 0.235 0.232 0.285 RANDOM 34.56
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] -0.31 0.92 0.09 0.72
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.49 r_dihedral_angle_3_deg 18.484 r_dihedral_angle_4_deg 14.157 r_dihedral_angle_1_deg 5.077 r_scangle_it 1.233 r_angle_refined_deg 1.038 r_mcangle_it 0.754 r_scbond_it 0.75 r_mcbond_it 0.5 r_nbtor_refined 0.292
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.49 r_dihedral_angle_3_deg 18.484 r_dihedral_angle_4_deg 14.157 r_dihedral_angle_1_deg 5.077 r_scangle_it 1.233 r_angle_refined_deg 1.038 r_mcangle_it 0.754 r_scbond_it 0.75 r_mcbond_it 0.5 r_nbtor_refined 0.292 r_nbd_refined 0.184 r_symmetry_vdw_refined 0.158 r_xyhbond_nbd_refined 0.122 r_symmetry_hbond_refined 0.074 r_chiral_restr 0.073 r_bond_refined_d 0.007 r_gen_planes_refined 0.002 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_refined 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_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 10600 Nucleic Acid Atoms Solvent Atoms 158 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing