3N1T

Crystal structure of the H101A mutant ecHint GMP complex


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3N1SPDB ENTRY 3N1S

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP729840% PEG 20000, 0.1M Magnesium Acetate, 0.1M Sodium Acetate, 20mM Tris pH 7.0, 1 mM EDTA, 10% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.1241.87

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 49.327α = 90
b = 64.066β = 109.04
c = 74.75γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray113CCDMARMOSAIC 325 mm CCDmirrors2006-06-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL9-10.975SSRLBL9-1

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
11.71637.788.20.083.441405413722231.6
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)
1.7161.7625.80.472.1

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 3N1S1.71635.3339308207587.650.196440.193870.24543RANDOM24.767
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]
-0.010.01-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.752
r_dihedral_angle_4_deg21.762
r_dihedral_angle_3_deg17.799
r_dihedral_angle_1_deg6.719
r_scangle_it4.146
r_scbond_it2.861
r_angle_refined_deg2.029
r_mcangle_it1.58
r_mcbond_it1.034
r_nbtor_refined0.314
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.752
r_dihedral_angle_4_deg21.762
r_dihedral_angle_3_deg17.799
r_dihedral_angle_1_deg6.719
r_scangle_it4.146
r_scbond_it2.861
r_angle_refined_deg2.029
r_mcangle_it1.58
r_mcbond_it1.034
r_nbtor_refined0.314
r_nbd_refined0.276
r_chiral_restr0.244
r_symmetry_vdw_refined0.209
r_xyhbond_nbd_refined0.195
r_symmetry_hbond_refined0.183
r_bond_refined_d0.018
r_gen_planes_refined0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3560
Nucleic Acid Atoms
Solvent Atoms317
Heterogen Atoms96

Software

Software
Software NamePurpose
HKL-2000data collection
MOLREPphasing
REFMACrefinement
DENZOdata reduction
SCALAdata scaling