X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1XMTPDB entry 1XMT

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP277PROTEIN SOLUTION (10 MG/ML PROTEIN, 0.050 M SODIUM CHLORIDE, 0.003 M SODIUM AZIDE, 0.0003 M TCEP, 0.005 M MES PH 6.0) MIXED IN A 1:1 RATIO WITH THE WELL SOLUTION (29% PEG 5000, 0.10 M SODIUM CITRATE, 0.10 M PIPES PH 6.5). CRYSTALS SOAKED 16 HOURS IN WELL SOLUTION SUPPLEMENTED WITH 0.009 M acetyl-Coenzyme. Crystals cryo-protected with fomblin 2500, vapor diffusion, hanging drop, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.2445.08

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 27.905α = 90
b = 63.941β = 90.86
c = 29.525γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315Double crystal monochromator, Si111, 2nd crystal sagital focus followed by Rh coated bent cylinder vertically focusing mirror2005-11-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 8-BM0.97949APS8-BM

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
12.0531.9899.20.05218.3034.36473
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)
12.052.1980.2514.9933.9432

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 REPLACEMENTTHROUGHOUTPDB entry 1XMT2.05431.976645863699.0950.1660.160.22RANDOM33.963
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]
0.7162.045-0.7010.046
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.241
r_dihedral_angle_4_deg16.802
r_dihedral_angle_3_deg16.084
r_scangle_it6.514
r_dihedral_angle_1_deg5.958
r_scbond_it4.882
r_mcangle_it2.621
r_angle_refined_deg1.664
r_mcbond_it1.608
r_nbtor_refined0.305
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.241
r_dihedral_angle_4_deg16.802
r_dihedral_angle_3_deg16.084
r_scangle_it6.514
r_dihedral_angle_1_deg5.958
r_scbond_it4.882
r_mcangle_it2.621
r_angle_refined_deg1.664
r_mcbond_it1.608
r_nbtor_refined0.305
r_nbd_refined0.207
r_xyhbond_nbd_refined0.163
r_symmetry_vdw_refined0.163
r_chiral_restr0.111
r_symmetry_hbond_refined0.083
r_bond_refined_d0.016
r_gen_planes_refined0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms728
Nucleic Acid Atoms
Solvent Atoms61
Heterogen Atoms48

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction