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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 55.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.249 α = 90 b = 106.104 β = 90 c = 128.206 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 CCD MAR CCD 165 mm mirror 2005-03-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X11 0.8162 EMBL/DESY, HAMBURG X11
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 1.25 15 100 0.057 19 3.5 83123 83123 -3 -3 11.7
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) 1.25 1.26 60 0.54 1.5 3.5 1596
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 adata PDB ENTRY 1QJ4 1.25 15 83123 83123 92.5 0.1273 0.1149 RANDOM 13
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 34 2013.38 2552.6
RMS Deviations Key Refinement Restraint Deviation s_approx_iso_adps 0.093 s_non_zero_chiral_vol 0.079 s_zero_chiral_vol 0.072 s_anti_bump_dis_restr 0.06 s_similar_adp_cmpnt 0.04 s_angle_d 0.028 s_from_restr_planes 0.0277 s_bond_d 0.012 s_rigid_bond_adp_cmpnt 0.004 s_similar_dist
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4328 Nucleic Acid Atoms Solvent Atoms 550 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