4FIO

Crystal Structure of Methenyltetrahydromethanopterin Cyclohydrolase from Methanobrevibacter ruminantium


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1QLMPDB ENTRY 1QLM

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION8.52930.2 M sodium acetate, 0.1 M Tris-HCl, 30% (w/v) PEG 4000 and 3% (v/v) isopropanol, pH 8.5, VAPOR DIFFUSION, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.1342.12

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 52.37α = 120.06
b = 74.855β = 100.01
c = 74.816γ = 98.28
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2011-04-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAUSTRALIAN SYNCHROTRON BEAMLINE MX2Australian SynchrotronMX2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.3719.8893.817.33.71845431
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.371.4479.60.6060.6062.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1QLM1.3719.88175155929993.70.1320.130.175RANDOM18.55
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]
2.070.72-1.55-0.444.45-1.63
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.407
r_sphericity_free19.25
r_dihedral_angle_4_deg16.144
r_dihedral_angle_3_deg13.995
r_sphericity_bonded10.757
r_rigid_bond_restr8.441
r_dihedral_angle_1_deg5.94
r_angle_refined_deg2.297
r_chiral_restr0.164
r_bond_refined_d0.023
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.407
r_sphericity_free19.25
r_dihedral_angle_4_deg16.144
r_dihedral_angle_3_deg13.995
r_sphericity_bonded10.757
r_rigid_bond_restr8.441
r_dihedral_angle_1_deg5.94
r_angle_refined_deg2.297
r_chiral_restr0.164
r_bond_refined_d0.023
r_gen_planes_refined0.014
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 AtomsNumber
Protein Atoms7144
Nucleic Acid Atoms
Solvent Atoms1071
Heterogen Atoms24

Software

Software
Software NamePurpose
Blu-Icedata collection
MOLREPphasing
REFMACrefinement
XDSdata reduction
SCALAdata scaling