3F47

The Crystal Structure of [Fe]-Hydrogenase (Hmd) Holoenzyme from Methanocaldococcus jannaschii


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3DAG 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.528350% MPD, 100mM Tris-HCl, 20mM Ammonium dihydrogen phosphate, 1mM DTT , pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 283K
Crystal Properties
Matthews coefficientSolvent content
2.4650.04

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 95.93α = 90
b = 95.93β = 90
c = 165.81γ = 90
Symmetry
Space GroupI 41 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCDDynamically bendable mirror2007-02-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA0.9920SLSX10SA

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
11.7526.295.50.056165.237583-332.677
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)
11.751.881.60.5082.63.69296

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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT3DAG1.752537574188795.630.1740.1730.205RANDOM33.553
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]
0.820.82-1.65
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.713
r_dihedral_angle_4_deg21.905
r_dihedral_angle_3_deg13.397
r_dihedral_angle_1_deg5.255
r_scangle_it3.978
r_scbond_it2.474
r_angle_refined_deg1.578
r_mcangle_it1.294
r_mcbond_it0.749
r_nbtor_refined0.302
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.713
r_dihedral_angle_4_deg21.905
r_dihedral_angle_3_deg13.397
r_dihedral_angle_1_deg5.255
r_scangle_it3.978
r_scbond_it2.474
r_angle_refined_deg1.578
r_mcangle_it1.294
r_mcbond_it0.749
r_nbtor_refined0.302
r_nbd_refined0.203
r_symmetry_vdw_refined0.196
r_symmetry_hbond_refined0.144
r_xyhbond_nbd_refined0.124
r_chiral_restr0.11
r_bond_refined_d0.016
r_gen_planes_refined0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2593
Nucleic Acid Atoms
Solvent Atoms238
Heterogen Atoms42

Software

Software
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
MAR345data collection
XDSdata reduction
REFMACphasing