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Crystal structure of geranylgeranyl diphosphate synthase sub1274 (target efi-509455) from streptococcus uberis 0140j with bound magnesium and isopentyl diphosphate, fully 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 2.52 51.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.385 α = 90 b = 74.326 β = 90 c = 124.473 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 1.76 50 99.3 0.107 8.6 6.1 65193 -5 17.703
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 1.76 1.79 89.8 0.665 2.8 5.6
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 1.76 46.67 63151 1973 99.69 0.15368 0.15274 0.1653 0.18354 0.1975 RANDOM 25.164
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] -0.26 1.97 -1.72
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.763 r_dihedral_angle_4_deg 14.211 r_dihedral_angle_3_deg 13.184 r_dihedral_angle_1_deg 4.442 r_angle_refined_deg 1.228 r_angle_other_deg 0.757 r_chiral_restr 0.068 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.763 r_dihedral_angle_4_deg 14.211 r_dihedral_angle_3_deg 13.184 r_dihedral_angle_1_deg 4.442 r_angle_refined_deg 1.228 r_angle_other_deg 0.757 r_chiral_restr 0.068 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 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_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4520 Nucleic Acid Atoms Solvent Atoms 538 Heterogen Atoms 62
Software Software Software Name Purpose PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling