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Crystal structure mutant H77A of human HD domain-containing protein 2, Genomics Consortium (NESG) Target HR6723
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4DMB PDB ENTRY 4DMB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 microbatch under oil 8 277 Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5) . Reservoir solution: 0.1M Mg(NO3)2, 0.1M Tris, 12% PEG 20000, microbatch under oil, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.67 53.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.38 α = 90 b = 71.38 β = 90 c = 199.308 γ = 90
Symmetry Space Group I 41 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 QUANTUM 4 mirrors 2012-11-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X4A 0.979 NSLS X4A
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 2.3 50 100 0.096 40.9 8.9 11866 -3 42.21
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT PDB ENTRY 4DMB 2.305 35.69 1.33 11843 562 99.97 0.1763 0.1739 0.1789 0.2281 0.2262 57.794
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 15.087 f_angle_d 1.101 f_chiral_restr 0.073 f_bond_d 0.008 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1520 Nucleic Acid Atoms Solvent Atoms 44 Heterogen Atoms 5
Software Software Software Name Purpose PHENIX refinement PDB_EXTRACT data extraction ADSC data collection HKL-2000 data reduction HKL-2000 data scaling BALBES phasing