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Crystal structure of the human UMP/CMP kinase in open conformation
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1UKE PDB ENTRY 1UKE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 298 PEG 4000, Magnesium Sulfate, Sodium Acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.9 57.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.75 α = 90 b = 62.75 β = 90 c = 226.31 γ = 120
Symmetry Space Group P 65 2 2
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 2002-11-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.0 APS 22-ID
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 2.1 30 94.5 0.116 15.27 13 15467 15467 -3 27.73075
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) 2.1 2.2 90.3 0.393 10.8 1737
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 PDB ENTRY 1UKE 2.1 15 14381 14381 1442 88.49 0.22168 0.22168 0.21574 0.2304 0.27473 0.2136 RANDOM 39.674
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] 0.14 0.07 0.14 -0.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.585 r_scangle_it 4.296 r_scbond_it 2.503 r_mcangle_it 1.751 r_angle_refined_deg 1.444 r_mcbond_it 0.905 r_angle_other_deg 0.867 r_nbd_other 0.231 r_symmetry_hbond_refined 0.222 r_xyhbond_nbd_refined 0.213
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.585 r_scangle_it 4.296 r_scbond_it 2.503 r_mcangle_it 1.751 r_angle_refined_deg 1.444 r_mcbond_it 0.905 r_angle_other_deg 0.867 r_nbd_other 0.231 r_symmetry_hbond_refined 0.222 r_xyhbond_nbd_refined 0.213 r_nbd_refined 0.21 r_symmetry_vdw_refined 0.207 r_symmetry_vdw_other 0.192 r_chiral_restr 0.091 r_nbtor_other 0.088 r_bond_refined_d 0.015 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1540 Nucleic Acid Atoms Solvent Atoms 111 Heterogen Atoms 5
Software Software Software Name Purpose REFMAC refinement MAR345 data collection XDS data scaling MOLREP phasing