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NIKR IN OPEN CONFORMATION AND NICKEL BOUND TO HIGH-AFFINITY SITES
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1Q5Y PDB ENTRY 1Q5Y
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 pH 7.50
Crystal Properties Matthews coefficient Solvent content 3.86 68.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.893 α = 90 b = 99.893 β = 90 c = 97.978 γ = 90
Symmetry Space Group P 41 21 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 IMAGE PLATE RIGAKU RAXIS-V 2004-04-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL26B1 SPring-8 BL26B1
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 3 30 99 0.06 20.8 9.4 10315 -1
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 3 3.11 98.8 0.29 4.8 5.6
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-Work (DCC) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1Q5Y 3 29.64 18601 877 98.1 0.237 0.237 0.2357 0.281 RANDOM 81.1
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] 10.59 10.59 -21.17
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 21.4 c_scangle_it 8.46 c_mcangle_it 6.12 c_scbond_it 5.72 c_mcbond_it 3.81 c_angle_deg 1.3 c_improper_angle_d 0.66 c_bond_d 0.007 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 21.4 c_scangle_it 8.46 c_mcangle_it 6.12 c_scbond_it 5.72 c_mcbond_it 3.81 c_angle_deg 1.3 c_improper_angle_d 0.66 c_bond_d 0.007 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2132 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 5
Software Software Software Name Purpose HKL-2000 data reduction HKL-2000 data scaling DM phasing CNS phasing CNS refinement