☰ Navigation Tabs
Crystal structure of human glycine decarboxylase (P-protein)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4LHD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 0.1 M HEPES pH 7, 6 % PEG3350, 10 mM DTT
Crystal Properties Matthews coefficient Solvent content 2.39 48.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.81 α = 90 b = 123.51 β = 97.87 c = 99.51 γ = 90
Symmetry Space Group P 1 21 1
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 2017-08-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-3 0.97 ESRF MASSIF-3
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) CC (Half) 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 2.3 46.1 99.3 0.079 0.99 12.3 4.5 90460 1
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 2.3 2.4 99.8 0.74 1.3 4.6
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 4LHD 2.3 46.08 85899 4521 99.18 0.2129 0.21168 0.2169 0.23549 0.2392 RANDOM 56.399
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] 1.82 1.29 -1.97 -0.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.242 r_dihedral_angle_4_deg 16.873 r_dihedral_angle_3_deg 14.149 r_dihedral_angle_1_deg 6.482 r_long_range_B_refined 6.25 r_long_range_B_other 6.249 r_angle_other_deg 3.749 r_angle_refined_deg 1.493 r_scangle_other 0.813 r_scbond_it 0.718
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.242 r_dihedral_angle_4_deg 16.873 r_dihedral_angle_3_deg 14.149 r_dihedral_angle_1_deg 6.482 r_long_range_B_refined 6.25 r_long_range_B_other 6.249 r_angle_other_deg 3.749 r_angle_refined_deg 1.493 r_scangle_other 0.813 r_scbond_it 0.718 r_scbond_other 0.718 r_mcangle_it 0.702 r_mcangle_other 0.702 r_mcbond_it 0.39 r_mcbond_other 0.39 r_chiral_restr 0.084 r_gen_planes_other 0.016 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 r_bond_other_d r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14617 Nucleic Acid Atoms Solvent Atoms 165 Heterogen Atoms 70
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing