1ZCZ | pdb_00001zcz

Crystal structure of Phosphoribosylaminoimidazolecarboxamide formyltransferase / IMP cyclohydrolase (TM1249) from THERMOTOGA MARITIMA at 1.88 A resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1M9N1m9n 1g8mA

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION,SITTING DROP,NANODROP529320.0% PEG-6000, 0.1M Citrate pH 5.0, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.346.12

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 62.084α = 99.26
b = 58.63β = 96.89
c = 72.749γ = 106.13
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210Single crystal, cylindrically bent, Si(220)2005-02-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.1ALS5.0.1

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
11.885095.60.05625.652.974289
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)
11.881.9170.670.60.3140.02051.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1m9n 1g8mA1.885069797370095.890.1580.158490.1560.170.1970.21RANDOM36.497
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]
-1.56-0.09-1.160.21-1.070.68
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.025
r_dihedral_angle_4_deg16.251
r_dihedral_angle_3_deg13.86
r_scangle_it6.267
r_dihedral_angle_1_deg5.785
r_scbond_it4.296
r_mcangle_it2.577
r_mcbond_it1.603
r_angle_refined_deg1.395
r_angle_other_deg0.985
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.025
r_dihedral_angle_4_deg16.251
r_dihedral_angle_3_deg13.86
r_scangle_it6.267
r_dihedral_angle_1_deg5.785
r_scbond_it4.296
r_mcangle_it2.577
r_mcbond_it1.603
r_angle_refined_deg1.395
r_angle_other_deg0.985
r_mcbond_other0.615
r_symmetry_vdw_other0.263
r_metal_ion_refined0.223
r_nbd_refined0.22
r_nbd_other0.178
r_nbtor_refined0.177
r_xyhbond_nbd_refined0.155
r_symmetry_hbond_refined0.098
r_chiral_restr0.087
r_nbtor_other0.084
r_symmetry_vdw_refined0.071
r_bond_refined_d0.013
r_gen_planes_refined0.006
r_bond_other_d0.005
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6961
Nucleic Acid Atoms
Solvent Atoms636
Heterogen Atoms28

Software

Software
Software NamePurpose
REFMACrefinement
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
DENZOdata reduction