7YC6

Crystal structure of D110P mutant of GATase subunit of Methanocaldococcus jannaschii GMP synthetase


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1MICROBATCH2980.2M Zinc acetate dihydrate, 20% PEG 3350, pH 6.4
Crystal Properties
Matthews coefficientSolvent content
2.8757.12

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 63.08α = 90
b = 63.08β = 90
c = 101.94γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray277IMAGE PLATEMAR scanner 345 mm plate2022-03-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODEBRUKER AXS MICROSTAR1.54179

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)CC (Half)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
12.454.631000.160.99516.112.89659
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.42.530.995

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 REPLACEMENTTHROUGHOUT7D402.454.6392074251000.199870.198850.22123RANDOM15.67
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]
0.20.10.2-0.66
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.421
r_dihedral_angle_3_deg17.156
r_dihedral_angle_4_deg14.061
r_dihedral_angle_1_deg6.938
r_long_range_B_refined4.575
r_long_range_B_other4.526
r_scangle_other2.873
r_angle_other_deg2.373
r_mcangle_it2.268
r_mcangle_other2.267
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.421
r_dihedral_angle_3_deg17.156
r_dihedral_angle_4_deg14.061
r_dihedral_angle_1_deg6.938
r_long_range_B_refined4.575
r_long_range_B_other4.526
r_scangle_other2.873
r_angle_other_deg2.373
r_mcangle_it2.268
r_mcangle_other2.267
r_scbond_it1.816
r_scbond_other1.815
r_angle_refined_deg1.594
r_mcbond_it1.38
r_mcbond_other1.36
r_chiral_restr0.078
r_bond_other_d0.036
r_bond_refined_d0.011
r_gen_planes_refined0.007
r_gen_planes_other0.007
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1386
Nucleic Acid Atoms
Solvent Atoms76
Heterogen Atoms6

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing