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Plant enzyme crystal form II
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1AFW PDB ENTRY 1AFW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.7 25% POLYETHYLENE GLYCOL 4000, 0.1M TRIS-HCL PH 8.5, 300MM MGCL2
Crystal Properties Matthews coefficient Solvent content 2.3 47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.395 α = 90 b = 95.821 β = 90 c = 56.125 γ = 90
Symmetry Space Group P 21 21 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 CCD M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 ESRF ID14-2
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 2.4 20 87.3 0.06 6.4 2.2 16453 53.6
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 2.4 2.5 69.9 0.3 1.1 2.2
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 THROUGHOUT PDB ENTRY 1AFW 2.37 18.54 13748 725 87.4 0.202 0.198 0.1975 0.276 0.2779 RANDOM 45.87
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] -0.52 -0.12 0.64
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.582 r_dihedral_angle_4_deg 18.396 r_dihedral_angle_3_deg 16.722 r_dihedral_angle_1_deg 5.644 r_scangle_it 1.883 r_angle_refined_deg 1.269 r_scbond_it 1.145 r_mcangle_it 0.806 r_mcbond_it 0.46 r_nbtor_refined 0.295
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.582 r_dihedral_angle_4_deg 18.396 r_dihedral_angle_3_deg 16.722 r_dihedral_angle_1_deg 5.644 r_scangle_it 1.883 r_angle_refined_deg 1.269 r_scbond_it 1.145 r_mcangle_it 0.806 r_mcbond_it 0.46 r_nbtor_refined 0.295 r_symmetry_vdw_refined 0.217 r_nbd_refined 0.196 r_xyhbond_nbd_refined 0.18 r_symmetry_hbond_refined 0.102 r_chiral_restr 0.086 r_bond_refined_d 0.01 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2900 Nucleic Acid Atoms Solvent Atoms 102 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing