3IK4 | pdb_00003ik4

CRYSTAL STRUCTURE OF mandelate racemase/muconate lactonizing protein from Herpetosiphon aurantiacus


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.5150MM POTASSIUM BROMIDE, PH 7.5, 30% PEG2000 MME, 10% GLYCEROL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K
Crystal Properties
Matthews coefficientSolvent content
2.0640.26

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 84.026α = 90
b = 93.344β = 112.6
c = 85.914γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray90CCDADSC QUANTUM 315MIRRORS2009-07-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X29ANSLSX29A

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
12.075098.90.0637.94.175228-543.053
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)
12.072.1491.20.780.93.7

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMRTHROUGHOUT1JPM2.12068809214799.370.218550.216760.220.275310.27RANDOM41.917
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]
-2.51-1.49-1.733.09
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.668
r_dihedral_angle_4_deg19.369
r_dihedral_angle_3_deg18.049
r_scangle_it12.844
r_scbond_it10.315
r_mcangle_it7.058
r_dihedral_angle_1_deg5.467
r_mcbond_it5.364
r_angle_refined_deg1.253
r_nbtor_refined0.291
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.668
r_dihedral_angle_4_deg19.369
r_dihedral_angle_3_deg18.049
r_scangle_it12.844
r_scbond_it10.315
r_mcangle_it7.058
r_dihedral_angle_1_deg5.467
r_mcbond_it5.364
r_angle_refined_deg1.253
r_nbtor_refined0.291
r_xyhbond_nbd_refined0.159
r_nbd_refined0.146
r_symmetry_hbond_refined0.138
r_symmetry_vdw_refined0.119
r_chiral_restr0.085
r_bond_refined_d0.009
r_gen_planes_refined0.004
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 Atoms10201
Nucleic Acid Atoms
Solvent Atoms237
Heterogen Atoms16

Software

Software
Software NamePurpose
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling