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HNL from Hevea brasiliensis to atomic resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1QJ4 PDB ENTRY 1QJ4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 2% PEG400, 2M ammonium sulphate, 0.1M Hepes-Na, pH7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.75 55.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.243 α = 90 b = 106.373 β = 90 c = 128.309 γ = 90
Symmetry Space Group C 2 2 21
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 MAR scanner 345 mm plate mirror 2005-03-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE BW7B 0.8430 EMBL/DESY, HAMBURG BW7B
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 1.05 30 100 0.046 26 3.9 140831 140831 -3 -3 8.2
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) 1.05 1.06 50 0.29 3.1 2 1721
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MR/rigid body placement FREE R initially, final refinement against all data PDB ENTRY 1QJ4 1.05 30 140831 140831 100 0.1087 0.1008 RANDOM 11
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]
Coordinate Error Structure Solution Method Refinement High Resolution Refinement Low Resolution 38 2040.7 2654.25
RMS Deviations Key Refinement Restraint Deviation s_anti_bump_dis_restr 0.101 s_non_zero_chiral_vol 0.099 s_approx_iso_adps 0.099 s_zero_chiral_vol 0.09 s_similar_adp_cmpnt 0.037 s_angle_d 0.03 s_from_restr_planes 0.0285 s_bond_d 0.016 s_rigid_bond_adp_cmpnt 0.006 s_similar_dist
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4415 Nucleic Acid Atoms Solvent Atoms 621 Heterogen Atoms 24
Software Software Software Name Purpose SHELX model building SHELXL-97 refinement MAR345 data collection DENZO data reduction SCALEPACK data scaling REFMAC phasing