4KQN

2.8 Angstrom Resolution Crystal Structure of D-Hydantoinase from Bacillus sp. AR9 in C2221 Space Group


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8298100mM Imidazole, 225mM CsCl, 15% PEG3350 , pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.3848.24

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 90.877α = 90
b = 185.239β = 90
c = 113.447γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray298IMAGE PLATEMARRESEARCHmirror2006-02-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU1.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.825.4188228291993021

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (I)Cut-off Sigma (F)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1yny2.825.41222282919930107987.640.209210.206060.26663RANDOM43.458
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]
0.03-0.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.444
r_dihedral_angle_4_deg21.75
r_dihedral_angle_3_deg20.269
r_dihedral_angle_1_deg7.634
r_angle_refined_deg1.614
r_angle_other_deg0.955
r_chiral_restr0.085
r_bond_refined_d0.013
r_gen_planes_refined0.008
r_bond_other_d0.004
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.444
r_dihedral_angle_4_deg21.75
r_dihedral_angle_3_deg20.269
r_dihedral_angle_1_deg7.634
r_angle_refined_deg1.614
r_angle_other_deg0.955
r_chiral_restr0.085
r_bond_refined_d0.013
r_gen_planes_refined0.008
r_bond_other_d0.004
r_gen_planes_other0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7051
Nucleic Acid Atoms
Solvent Atoms13
Heterogen Atoms4

Software

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