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Crystal structure of APE1195
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2GKS PDB ENTRY 2GKS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 oil batch 7.6 293 15% (v/v) MPD, 0.1M HEPES-NaOH, 0.2M tri-Na Citr, pH 7.6, oil batch, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.42 49.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.01 α = 90 b = 102.82 β = 96.67 c = 45.58 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 RIGAKU JUPITER 210 2007-03-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL26B2 1.00000 SPring-8 BL26B2
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 2.1 50 98.8 0.045 31.2 5.3 23374 23213 -3 22.2
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 2.1 2.18 91.3 0.159 5.4 4.4 2117
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 PDB ENTRY 2GKS 2.1 45.27 23094 1160 98.7 0.202 0.202 0.2041 0.249 0.2058 RANDOM 38.3
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] -0.66 -0.77 -8.35 9.01
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 21.9 c_scangle_it 6.78 c_scbond_it 5.25 c_mcangle_it 4.55 c_mcbond_it 3.45 c_angle_deg 1.4 c_improper_angle_d 0.89 c_bond_d 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2807 Nucleic Acid Atoms Solvent Atoms 131 Heterogen Atoms
Software Software Software Name Purpose CNS refinement HKL-2000 data collection HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing