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X-ray structure of the Archaeoglobus fulgidus methenyl-tetrahydromethanopterin cyclohydrolase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1QLM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 291 10% (w/v) PEG 4000, 10% (v/v) Isopropanol, 0.1M Sodium acetate pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.71 54.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 118.54 α = 90 b = 122.08 β = 99.02 c = 79.39 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 2011-12-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 1.0001 SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.52 48.17 170753 164493
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 1QLM 1.52 48.17 156241 8252 96.33 0.16754 0.16425 0.1626 0.23124 0.2312 RANDOM 25.003
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] 0.39 0.17 -0.16 -0.17
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 39.415 r_dihedral_angle_2_deg 35.563 r_sphericity_bonded 22.006 r_dihedral_angle_4_deg 20.294 r_dihedral_angle_3_deg 14.329 r_dihedral_angle_1_deg 6.863 r_rigid_bond_restr 5.309 r_angle_refined_deg 1.89 r_chiral_restr 0.145 r_bond_refined_d 0.018
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 39.415 r_dihedral_angle_2_deg 35.563 r_sphericity_bonded 22.006 r_dihedral_angle_4_deg 20.294 r_dihedral_angle_3_deg 14.329 r_dihedral_angle_1_deg 6.863 r_rigid_bond_restr 5.309 r_angle_refined_deg 1.89 r_chiral_restr 0.145 r_bond_refined_d 0.018 r_gen_planes_refined 0.011 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7308 Nucleic Acid Atoms Solvent Atoms 740 Heterogen Atoms
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement XDS data reduction XSCALE data scaling