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Crystal structure of human uridine-cytidine kinase 1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1RXJ PDB ENTRY 1RXJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 0.8-1.0 M SUCCINIC ACID PH 6.7-7.3
Crystal Properties Matthews coefficient Solvent content 2.6 53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.971 α = 90 b = 67.971 β = 90 c = 236.1 γ = 120
Symmetry Space Group P 62 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 ADSC CCD 2006-10-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 ESRF ID14-1
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 30 99.9 0.09 25.4 18.6 12014 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 0.46 7.2 17.4
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 1RXJ 2.5 29.45 11402 572 99.9 0.205 0.204 0.24 RANDOM 20.91
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] -0.09 -0.04 -0.09 0.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.421 r_dihedral_angle_4_deg 19.975 r_dihedral_angle_3_deg 16.821 r_dihedral_angle_1_deg 5.009 r_scangle_it 2.508 r_scbond_it 1.689 r_mcangle_it 1.302 r_angle_refined_deg 1.191 r_mcbond_it 0.732 r_nbtor_refined 0.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.421 r_dihedral_angle_4_deg 19.975 r_dihedral_angle_3_deg 16.821 r_dihedral_angle_1_deg 5.009 r_scangle_it 2.508 r_scbond_it 1.689 r_mcangle_it 1.302 r_angle_refined_deg 1.191 r_mcbond_it 0.732 r_nbtor_refined 0.305 r_symmetry_hbond_refined 0.235 r_nbd_refined 0.203 r_symmetry_vdw_refined 0.14 r_xyhbond_nbd_refined 0.139 r_chiral_restr 0.082 r_bond_refined_d 0.01 r_gen_planes_refined 0.003 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 1715 Nucleic Acid Atoms Solvent Atoms 41 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing