5YGA

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


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, 0.1% Low Melting Agarose
Crystal Properties
Matthews coefficientSolvent content
3.3162.84

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 98.8α = 90
b = 98.8β = 90
c = 256.431γ = 120
Symmetry
Space GroupP 31 1 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++VariMax HF2017-03-21MSINGLE 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
12.4585.561000.1090.1130.0320.99919.612.653172

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 REPLACEMENTTHROUGHOUT5YFJ2.4585.5650474261899.980.17040.16750.2253RANDOM41.908
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]
1.220.611.22-3.96
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.258
r_dihedral_angle_4_deg19.224
r_dihedral_angle_3_deg16.614
r_dihedral_angle_1_deg6.514
r_angle_refined_deg1.822
r_angle_other_deg1.021
r_chiral_restr0.098
r_bond_refined_d0.016
r_gen_planes_refined0.008
r_bond_other_d0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.258
r_dihedral_angle_4_deg19.224
r_dihedral_angle_3_deg16.614
r_dihedral_angle_1_deg6.514
r_angle_refined_deg1.822
r_angle_other_deg1.021
r_chiral_restr0.098
r_bond_refined_d0.016
r_gen_planes_refined0.008
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7638
Nucleic Acid Atoms
Solvent Atoms301
Heterogen Atoms

Software

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