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Crystal structure of human glycine decarboxylase (P-protein) bound with pyridoxyl-glycine-5'-monophosphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6I33
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 0.1 M HEPES pH 7, 6 % PEG3350, 10 mM DTT
Crystal Properties Matthews coefficient Solvent content 2.38 48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.66 α = 90 b = 123.44 β = 97.93 c = 197.67 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 2017-09-14 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 49.33 99 0.17 0.995 5.3 4.6 271538
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 2.1 98.8 0.484 1.1 4.5
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 6I33 2 49.33 257933 13576 98.99 0.21627 0.215 0.222 0.24047 0.2454 RANDOM 47.125
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] -2.71 2.96 0.75 1.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.214 r_dihedral_angle_4_deg 17.064 r_dihedral_angle_3_deg 13.713 r_dihedral_angle_1_deg 6.733 r_long_range_B_refined 5.241 r_long_range_B_other 5.24 r_scangle_other 2.252 r_mcangle_other 1.803 r_mcangle_it 1.802 r_scbond_it 1.453
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.214 r_dihedral_angle_4_deg 17.064 r_dihedral_angle_3_deg 13.713 r_dihedral_angle_1_deg 6.733 r_long_range_B_refined 5.241 r_long_range_B_other 5.24 r_scangle_other 2.252 r_mcangle_other 1.803 r_mcangle_it 1.802 r_scbond_it 1.453 r_scbond_other 1.45 r_angle_other_deg 1.445 r_angle_refined_deg 1.341 r_mcbond_it 1.134 r_mcbond_other 1.134 r_chiral_restr 0.082 r_bond_refined_d 0.011 r_gen_planes_other 0.011 r_gen_planes_refined 0.008 r_bond_other_d 0.001 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 29750 Nucleic Acid Atoms Solvent Atoms 1024 Heterogen Atoms 158
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing