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Crystal structure of geranylgeranyl diphosphate synthase sub1274 (target efi-509455) from streptococcus uberis 0140j with bound magnesium and isopentyl diphosphate, partially liganded complex;
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4GP1 PDB ENTRY 4GP1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 0.2M MAGNESIUM CHLORIDE, 0.1M MES-NAOH, PH 6.5, 25% PEG4000, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K
Crystal Properties Matthews coefficient Solvent content 2.59 52.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.798 α = 90 b = 75.789 β = 90 c = 124.62 γ = 90
Symmetry Space Group P 21 21 21
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 315 MIRRORS 2013-04-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A 1.075 NSLS X29A
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 1.95 50 98.8 0.082 12.6 8.2 48833 -5 24.882
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 1.95 1.98 100 0.52 4.1 7.7
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 PDB ENTRY 4GP1 1.95 46.82 46768 1510 97.72 0.20794 0.20698 0.2137 0.23631 0.2411 RANDOM 37.708
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] -2.73 6.54 -3.81
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.717 r_dihedral_angle_3_deg 14.481 r_dihedral_angle_4_deg 14.256 r_long_range_B_other 11.216 r_long_range_B_refined 11.17 r_scangle_other 10.537 r_scbond_it 8.448 r_scbond_other 8.447 r_mcangle_other 6.165 r_mcangle_it 6.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.717 r_dihedral_angle_3_deg 14.481 r_dihedral_angle_4_deg 14.256 r_long_range_B_other 11.216 r_long_range_B_refined 11.17 r_scangle_other 10.537 r_scbond_it 8.448 r_scbond_other 8.447 r_mcangle_other 6.165 r_mcangle_it 6.16 r_mcbond_it 5.185 r_mcbond_other 5.172 r_dihedral_angle_1_deg 4.683 r_angle_refined_deg 1.091 r_angle_other_deg 0.728 r_chiral_restr 0.059 r_bond_refined_d 0.006 r_gen_planes_refined 0.004 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 4368 Nucleic Acid Atoms Solvent Atoms 226 Heterogen Atoms 47
Software Software Software Name Purpose PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling