3NO4

Crystal structure of a creatinine amidohydrolase (Npun_F1913) from Nostoc punctiforme PCC 73102 at 2.00 A resolution


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.62770.2000M (NH4)2Tartrate, 20.0000% PEG-3350, No Buffer pH 6.6, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.3948.59

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 89.085α = 90
b = 89.085β = 90
c = 211.563γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 325 mm CCDFLAT MIRROR (VERTICAL FOCUSING)2009-12-03MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL11-10.91837,0.97939,0.97901SSRLBL11-1

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
1229.69599.90.1649.97.35847520.76
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)
22.0599.90.9432.4

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 DIFFRACTIONMADTHROUGHOUT229.6955839929551000.1530.1510.192RANDOM28.72
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]
1.151.15-2.3
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.522
r_dihedral_angle_4_deg17.489
r_dihedral_angle_3_deg13.051
r_dihedral_angle_1_deg6.297
r_scangle_it3.217
r_scbond_it2.078
r_angle_refined_deg1.536
r_angle_other_deg1.306
r_mcangle_it1.188
r_mcbond_it0.685
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.522
r_dihedral_angle_4_deg17.489
r_dihedral_angle_3_deg13.051
r_dihedral_angle_1_deg6.297
r_scangle_it3.217
r_scbond_it2.078
r_angle_refined_deg1.536
r_angle_other_deg1.306
r_mcangle_it1.188
r_mcbond_it0.685
r_mcbond_other0.204
r_chiral_restr0.092
r_bond_refined_d0.017
r_gen_planes_refined0.007
r_bond_other_d0.003
r_gen_planes_other0.002
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5863
Nucleic Acid Atoms
Solvent Atoms581
Heterogen Atoms76

Software

Software
Software NamePurpose
REFMACrefinement
PHENIXrefinement
SOLVEphasing
MolProbitymodel building
SCALAdata scaling
PDB_EXTRACTdata extraction
MOSFLMdata reduction