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Crystal structure of human HMG box-containing protein 1, HBP1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1V06 pdb entry 1V06
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 277.15 25% PEG 3350, 0.3M Ammonium sulfate, 0.1M Bis-Tris, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 277.15K
Crystal Properties Matthews coefficient Solvent content 4.09 69.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 118.84 α = 90 b = 118.84 β = 90 c = 93.19 γ = 120
Symmetry Space Group P 31 2 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 Q315 3x3 CCD Kirkpatrick Baez bimorph mirror pair 2010-06-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.9795 Diamond I02
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 2.04 59.42 99.5 0.097 11.1 5.7 48373 48353 33.9
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) 2.04 2.15 97.1 0.757 2.1 5.2 6798
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Number Reflections (All) 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 1V06 2.04 35.9 2 48353 46301 2051 99.4 0.1637 0.16243 0.1645 0.19175 0.19 RANDOM 31.142
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] -0.69 -0.35 -0.69 1.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.53 r_dihedral_angle_4_deg 19.602 r_dihedral_angle_3_deg 13.687 r_scangle_it 8.476 r_scbond_it 6.653 r_dihedral_angle_1_deg 6.35 r_mcangle_it 4.333 r_mcbond_it 2.67 r_angle_refined_deg 1.557 r_mcbond_other 1.55
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.53 r_dihedral_angle_4_deg 19.602 r_dihedral_angle_3_deg 13.687 r_scangle_it 8.476 r_scbond_it 6.653 r_dihedral_angle_1_deg 6.35 r_mcangle_it 4.333 r_mcbond_it 2.67 r_angle_refined_deg 1.557 r_mcbond_other 1.55 r_angle_other_deg 0.897 r_chiral_restr 0.094 r_bond_refined_d 0.016 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3009 Nucleic Acid Atoms Solvent Atoms 396 Heterogen Atoms 155
Software Software Software Name Purpose GDA data collection PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling