5YFX

Crystal structure of ribose-1,5-bisphosphate isomerase mutant D204N from Pyrococcus horikoshii OT3 in complex with ribose-1,5-bisphosphate and AMP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5YFJ 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2930.7 M NaCl, 3% PEG 6000, 20% MPD
Crystal Properties
Matthews coefficientSolvent content
2.6152.98

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 81.13α = 90
b = 81.13β = 90
c = 100.18γ = 120
Symmetry
Space GroupP 3 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++VariMax HF2016-11-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)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
12.7100.181000.090.0940.0290.9982310.310900

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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT5YFJ2.7100.181034855299.990.18090.17650.2644RANDOM48.382
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]
-1.85-0.93-1.856.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.624
r_dihedral_angle_4_deg21.581
r_dihedral_angle_3_deg17.002
r_dihedral_angle_1_deg6.875
r_angle_refined_deg1.651
r_angle_other_deg0.961
r_chiral_restr0.085
r_bond_refined_d0.011
r_gen_planes_refined0.006
r_bond_other_d0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.624
r_dihedral_angle_4_deg21.581
r_dihedral_angle_3_deg17.002
r_dihedral_angle_1_deg6.875
r_angle_refined_deg1.651
r_angle_other_deg0.961
r_chiral_restr0.085
r_bond_refined_d0.011
r_gen_planes_refined0.006
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2538
Nucleic Acid Atoms
Solvent Atoms45
Heterogen Atoms41

Software

Software
Software NamePurpose
HKL-3000data collection
MOSFLMdata processing
Aimlessdata scaling
PHASERphasing
REFMACrefinement
Cootmodel building
PDB_EXTRACTdata extraction