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Crystal structure of isoprenoid synthase A3MSH1 (TARGET EFI-501992) from Pyrobaculum calidifontis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1WY0 PDB ENTRY 1WY0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.5 0.1M BIS-TRIS, 25% PEG3350, PH 5.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294
Crystal Properties Matthews coefficient Solvent content 2.56 52.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.401 α = 90 b = 89.269 β = 90 c = 149.542 γ = 90
Symmetry Space Group C 2 2 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 2011-11-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A NSLS X29A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.65 70 93.8 0.117 9.9 7.7 49409 -5 22.442
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 1.65 1.68 100 0.36 3.8 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 PDB ENTRY 1WY0 1.65 50 44552 1430 93.07 0.18162 0.18062 0.1801 0.21252 0.2111 RANDOM 27.387
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] 2.27 -1.65 -0.62
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.446 r_dihedral_angle_4_deg 14.586 r_dihedral_angle_3_deg 12.073 r_dihedral_angle_1_deg 4.26 r_angle_refined_deg 1.26 r_chiral_restr 0.075 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.446 r_dihedral_angle_4_deg 14.586 r_dihedral_angle_3_deg 12.073 r_dihedral_angle_1_deg 4.26 r_angle_refined_deg 1.26 r_chiral_restr 0.075 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_scbond_it 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 2564 Nucleic Acid Atoms Solvent Atoms 316 Heterogen Atoms 10
Software Software Software Name Purpose PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling