☰ Navigation Tabs
X-ray structure of the Archaeoglobus fulgidus methenyl-tetrahydromethanopterin cyclohydrolase in complex with N5-formyl-tetrahydromethanopterin
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 4.6 291 8% (w/v) PEG 4000, 0.1M ammonium acetate, 0.1M sodium acetate pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.75 55.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.9 α = 90 b = 108.99 β = 90 c = 114.91 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 2010-04-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 1.214 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 1.75 43.402 116728 108423
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 1.75 43.4 103000 5423 92.94 0.18902 0.18718 0.1864 0.22421 0.2232 RANDOM 28.853
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.222 r_dihedral_angle_4_deg 17.193 r_dihedral_angle_3_deg 15.014 r_dihedral_angle_1_deg 6.12 r_angle_refined_deg 1.971 r_chiral_restr 0.152 r_bond_refined_d 0.019 r_gen_planes_refined 0.011 r_bond_other_d r_angle_other_deg
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.222 r_dihedral_angle_4_deg 17.193 r_dihedral_angle_3_deg 15.014 r_dihedral_angle_1_deg 6.12 r_angle_refined_deg 1.971 r_chiral_restr 0.152 r_bond_refined_d 0.019 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7308 Nucleic Acid Atoms Solvent Atoms 510 Heterogen Atoms 55
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement XDS data reduction XSCALE data scaling