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Crystal structure of a cupin protein (tm1459) in apo form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1VJ2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 25% Jeffamine ED-2001, 0.1M MES
Crystal Properties Matthews coefficient Solvent content 2.02 39.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.587 α = 90 b = 57.591 β = 90 c = 74.643 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 2016-07-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.9 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 1.2 50 99.3 0.087 20.5 7 68873
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.2 1.25 98.8 0.721 2.3 7.2 3325
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 (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 1vj2 1.2 50 64882 3446 100 0.1578 0.1575 0.1531 0.201 0.194 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]
Coordinate Error Structure Solution Method Refinement High Resolution Refinement Low Resolution 133 2084.4
RMS Deviations Key Refinement Restraint Deviation s_non_zero_chiral_vol 0.705 s_approx_iso_adps 0.133 s_zero_chiral_vol 0.084 s_similar_adp_cmpnt 0.028 s_angle_d 0.022 s_anti_bump_dis_restr 0.012 s_bond_d 0.007 s_from_restr_planes 0.004 s_similar_dist s_rigid_bond_adp_cmpnt
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1936 Nucleic Acid Atoms Solvent Atoms 328 Heterogen Atoms 16
Software Software Software Name Purpose PHASER phasing HKL-2000 data reduction HKL-2000 data scaling SHELX phasing SHELXL-97 refinement SHELXL phasing