2QV6

GTP cyclohydrolase III from M. jannaschii (MJ0145) complexed with GTP and metal ions


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.529217% PEG 4000, 0.2 M sodium acetate, 0.1 M Tris buffer, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Crystal Properties
Matthews coefficientSolvent content
2.4449.53

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 100.203α = 90
b = 129.578β = 90
c = 90.876γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray295IMAGE PLATERIGAKU RAXIS IV++confocal blue2007-06-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RUH3R1.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
1231.394.60.0838.73.97617225.7
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
22.0792.70.4222.93.67350

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONMADTHROUGHOUT231.3172282384594.570.208290.206320.24431RANDOM26.675
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]
-0.662.11-1.45
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.075
r_dihedral_angle_4_deg23.942
r_dihedral_angle_3_deg16.032
r_dihedral_angle_1_deg5.954
r_scangle_it3.245
r_scbond_it2.063
r_angle_refined_deg1.523
r_mcangle_it1.247
r_angle_other_deg0.979
r_mcbond_it0.666
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.075
r_dihedral_angle_4_deg23.942
r_dihedral_angle_3_deg16.032
r_dihedral_angle_1_deg5.954
r_scangle_it3.245
r_scbond_it2.063
r_angle_refined_deg1.523
r_mcangle_it1.247
r_angle_other_deg0.979
r_mcbond_it0.666
r_nbd_refined0.232
r_symmetry_vdw_other0.212
r_nbd_other0.196
r_nbtor_refined0.174
r_xyhbond_nbd_refined0.156
r_metal_ion_refined0.151
r_mcbond_other0.14
r_symmetry_hbond_refined0.088
r_chiral_restr0.086
r_nbtor_other0.086
r_symmetry_vdw_refined0.082
r_bond_refined_d0.014
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8049
Nucleic Acid Atoms
Solvent Atoms193
Heterogen Atoms140

Software

Software
Software NamePurpose
CrystalCleardata collection
SOLVEphasing
REFMACrefinement
CrystalCleardata reduction
CrystalCleardata scaling