☰ Navigation Tabs
Crystal structure of PHGDH in complex with compound 9
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, 0.2M Lithium sulphate
Crystal Properties Matthews coefficient Solvent content 2.55 51.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.351 α = 90 b = 112.041 β = 96.04 c = 69.116 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 PILATUS 2M-F 2014-08-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1.000 SLS X06DA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.15 112.04 99.6 0.075 0.084 0.038 0.998 14.5 4.8 35486 29.3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.15 2.63 99.7 0.211 0.237 0.107 0.979 4.8
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 2.15 40 34428 1682 96.6 0.225 0.222 0.2236 0.276 0.2794 RANDOM 36.07
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] 2.5345 -0.1684 -4.6424 2.1079
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 18.78 t_omega_torsion 2.56 t_angle_deg 1.09 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 18.78 t_omega_torsion 2.56 t_angle_deg 1.09 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 4474 Nucleic Acid Atoms Solvent Atoms 576 Heterogen Atoms 41
Software Software Software Name Purpose Aimless data scaling BUSTER refinement PDB_EXTRACT data extraction TRUNCATE data reduction PHASER phasing