4YT4

Iron guanylylpyridinol (FeGP) cofactor-reconstituted HmdII from Methanocaldococcus jannaschii


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
otherHmdII from M. jannaschii

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.228150% (v/v) PEG200, 0.1 M Na/K-phosphate, 0.2 M NaCl
Crystal Properties
Matthews coefficientSolvent content
2.2144.23

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 59.81α = 90
b = 59.81β = 90
c = 183.43γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELPSI PILATUS 6M2013-08-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA1.000SLSX10SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)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
12.25099.50.0840.08817.1710.117675-340.04
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.22.396.60.3150.3743.7

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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTHmdII from M. jannaschii2.242.761678888499.510.18660.18450.2255RANDOM40.909
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]
0.180.18-0.36
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.414
r_dihedral_angle_4_deg24.481
r_dihedral_angle_3_deg17.506
r_dihedral_angle_1_deg6.371
r_scbond_it2.871
r_mcangle_it2.304
r_angle_refined_deg1.896
r_mcbond_it1.413
r_chiral_restr0.127
r_bond_refined_d0.014
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.414
r_dihedral_angle_4_deg24.481
r_dihedral_angle_3_deg17.506
r_dihedral_angle_1_deg6.371
r_scbond_it2.871
r_mcangle_it2.304
r_angle_refined_deg1.896
r_mcbond_it1.413
r_chiral_restr0.127
r_bond_refined_d0.014
r_gen_planes_refined0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2605
Nucleic Acid Atoms
Solvent Atoms108
Heterogen Atoms42

Software

Software
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
MOLREPphasing