1VRD

Crystal structure of Inosine-5'-monophosphate dehydrogenase (TM1347) from THERMOTOGA MARITIMA at 2.18 A resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1ZFJ 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION,SITTING DROP,NANODROP427340% MPD, 0.1M citric acid pH 4.0, final pH 4, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 273K
Crystal Properties
Matthews coefficientSolvent content
3.867.42

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 120.083α = 90
b = 120.083β = 90
c = 144.079γ = 90
Symmetry
Space GroupI 4

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC2001-10-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.3ALS5.0.3

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
12.1846.1294.490.07814.264.115004344.79
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.182.275.520.5741.513.261308

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 REPLACEMENTTHROUGHOUT1zfj2.1846.1247472255394.220.218630.216530.25759RANDOM39.358
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]
-2.2-2.24.41
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.071
r_dihedral_angle_4_deg16.725
r_dihedral_angle_3_deg15.276
r_scangle_it8.37
r_scbond_it6.057
r_dihedral_angle_1_deg5.935
r_mcangle_it3.083
r_mcbond_it2.073
r_angle_refined_deg1.523
r_nbtor_refined0.308
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.071
r_dihedral_angle_4_deg16.725
r_dihedral_angle_3_deg15.276
r_scangle_it8.37
r_scbond_it6.057
r_dihedral_angle_1_deg5.935
r_mcangle_it3.083
r_mcbond_it2.073
r_angle_refined_deg1.523
r_nbtor_refined0.308
r_symmetry_vdw_refined0.215
r_nbd_refined0.213
r_symmetry_hbond_refined0.188
r_xyhbond_nbd_refined0.158
r_chiral_restr0.092
r_bond_refined_d0.015
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4670
Nucleic Acid Atoms
Solvent Atoms206
Heterogen Atoms

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement