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Crystal structure of PHGDH in complex with BI-4924
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2G76
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.6 277 25 % PEG 8000, 0.1 M MES, 0.2 M Lithium sulphate
Crystal Properties Matthews coefficient Solvent content 2.24 45.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.137 α = 90 b = 111.959 β = 90.99 c = 62.505 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 CCD RIGAKU 2016-09-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE RIGAKU MICROMAX-003 1.541800
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Rrim I (All) Rpim 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 1.984 62.496 98.6 0.153 0.153 0.182 0.097 0.982 6.7 3.3 40459 18.49
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.984 1.991 91.7 0.57 0.57 0.662 0.373 0.512 2.1 2.7
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 2G76 1.984 39.6 40425 2052 98 0.263 0.262 0.2583 0.298 0.29 RANDOM 21.5
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] 1.9682 0.373 -1.2258 -0.7424
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 19.89 t_omega_torsion 2.34 t_angle_deg 1.01 t_bond_d 0.008 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 19.89 t_omega_torsion 2.34 t_angle_deg 1.01 t_bond_d 0.008 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_pseud_angle t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3099 Nucleic Acid Atoms Solvent Atoms 180 Heterogen Atoms 64
Software Software Software Name Purpose Aimless data scaling BUSTER refinement PDB_EXTRACT data extraction