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Crystal structure of a cupin protein (tm1459) in zinc (Zn) substituted form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5WSD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 293 25%(w/v) Jeffamine ED-2001, 0.1 M MES
Crystal Properties Matthews coefficient Solvent content 2.08 40.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.598 α = 90 b = 57.871 β = 90 c = 74.65 γ = 90
Symmetry Space Group P 21 21 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 RAYONIX MX300HE 2016-05-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.900 SPring-8 BL44XU
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 1.12 50 99.8 0.084 21.76 7 85007
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 1.12 1.14 100 0.757 2.64 7
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 (All) 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 FREE R-VALUE 5WSD 1.12 30 84933 4251 99.8 0.1388 0.1388 0.138 0.1281 0.1767 0.1632 RANDOM
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 s_non_zero_chiral_vol 0.6639 s_from_restr_planes 0.4097 s_approx_iso_adps 0.1467 s_zero_chiral_vol 0.0768 s_similar_adp_cmpnt 0.0444 s_rigid_bond_adp_cmpnt 0.0251 s_angle_d 0.0248 s_bond_d 0.0105 s_similar_dist s_anti_bump_dis_restr
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3723 Nucleic Acid Atoms Solvent Atoms 342 Heterogen Atoms 2
Software Software Software Name Purpose HKL-2000 data reduction HKL-2000 data scaling PHASER phasing SHELXL refinement