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PGK1 in complex with CRT0063465 (3-[2-(4-bromophenyl)-5,7-dimethyl-pyrazolo[1,5-a]pyrimidin-6-yl]propanoic acid)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2ZGV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291 2.4-2.8M Sodium potassium phosphate, pH 7.4 - 8.2, 10mM DTT
Crystal Properties Matthews coefficient Solvent content 2.07 40.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.87 α = 90 b = 103.9 β = 99.1 c = 50.65 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 ADSC QUANTUM 4r 2010-07-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9763 Diamond I04
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 1.9 30 98.1 0.07 18.5 6.7 28225
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 2 96.7 0.358 6.5
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2ZGV 1.9 28 26787 1410 97.78 0.17074 0.16792 0.22183 0.2307 RANDOM 24.778
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] -0.98 -0.16 0.53 0.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.525 r_dihedral_angle_4_deg 15.776 r_dihedral_angle_3_deg 13.54 r_dihedral_angle_1_deg 6.546 r_long_range_B_refined 6.174 r_long_range_B_other 6.171 r_scangle_other 4.457 r_mcangle_other 3.324 r_mcangle_it 3.323 r_scbond_it 3.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.525 r_dihedral_angle_4_deg 15.776 r_dihedral_angle_3_deg 13.54 r_dihedral_angle_1_deg 6.546 r_long_range_B_refined 6.174 r_long_range_B_other 6.171 r_scangle_other 4.457 r_mcangle_other 3.324 r_mcangle_it 3.323 r_scbond_it 3.002 r_scbond_other 2.98 r_mcbond_it 2.325 r_mcbond_other 2.323 r_angle_refined_deg 1.972 r_angle_other_deg 0.916 r_chiral_restr 0.112 r_bond_refined_d 0.019 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 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 2967 Nucleic Acid Atoms Solvent Atoms 234 Heterogen Atoms 46
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing