2PK3 | pdb_00002pk3

Crystal Structure of a GDP-4-keto-6-deoxy-D-mannose reductase


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.529835% pentaerythritol propoxylate (5/4 PO/OH), 100 mM Tris, 200 mM NaCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.7655.45

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 46.882α = 72.54
b = 55.744β = 82.95
c = 79.244γ = 75.61
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mm2005-10-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 5ID-B1.0APS5ID-B

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
11.8229.896.60.07613.464129-328.9
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)
11.821.8995.20.433.76792

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1rpn1.8229.796092232071000.166490.16480.160.19890.2RANDOM22.423
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]
-0.11-0.040.720.2-0.3-0.06
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.509
r_dihedral_angle_4_deg19.139
r_dihedral_angle_3_deg13.678
r_dihedral_angle_1_deg5.808
r_scangle_it3.547
r_scbond_it2.31
r_angle_refined_deg1.476
r_mcangle_it1.35
r_mcbond_it0.877
r_nbtor_refined0.302
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.509
r_dihedral_angle_4_deg19.139
r_dihedral_angle_3_deg13.678
r_dihedral_angle_1_deg5.808
r_scangle_it3.547
r_scbond_it2.31
r_angle_refined_deg1.476
r_mcangle_it1.35
r_mcbond_it0.877
r_nbtor_refined0.302
r_nbd_refined0.211
r_symmetry_vdw_refined0.208
r_symmetry_hbond_refined0.207
r_xyhbond_nbd_refined0.14
r_chiral_restr0.096
r_bond_refined_d0.014
r_gen_planes_refined0.005
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 Atoms4810
Nucleic Acid Atoms
Solvent Atoms350
Heterogen Atoms158

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
MrBUMPphasing