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Crystal structure of L-histidine decarboxylase (C57S/C101V/C282V mutant) from Photobacterium phosphoreum
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3F9T
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.5 293 PEG1000, sodium acetate
Crystal Properties Matthews coefficient Solvent content 3.39 63.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 114.166 α = 90 b = 114.166 β = 90 c = 151.191 γ = 120
Symmetry Space Group P 61 2 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 PIXEL DECTRIS EIGER X 4M 2017-05-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-1A 1.100 Photon Factory BL-1A
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 2.5 37.81 99.3 0.139 19.3 12.6 20646
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 2.5 2.54 0.968
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 3F9T 2.5 37.81 19546 1060 99.29 0.1865 0.1837 0.1908 0.2389 0.2422 RANDOM 31.858
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] -1.21 -0.6 -1.21 3.91
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.426 r_dihedral_angle_3_deg 17.402 r_dihedral_angle_4_deg 16.979 r_dihedral_angle_1_deg 7.221 r_angle_refined_deg 1.658 r_angle_other_deg 1.299 r_chiral_restr 0.076 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.426 r_dihedral_angle_3_deg 17.402 r_dihedral_angle_4_deg 16.979 r_dihedral_angle_1_deg 7.221 r_angle_refined_deg 1.658 r_angle_other_deg 1.299 r_chiral_restr 0.076 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2975 Nucleic Acid Atoms Solvent Atoms 108 Heterogen Atoms 5
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling HKL-2000 data collection MOLREP phasing HKL-2000 data reduction