X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3GB5PDB entry 3GB5

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.52930.2M Ammonium acetate, 45% 2-Methyl-2,4-pentanediol, 0.1M Bis-Tris pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.2545.26

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.61α = 90
b = 112.567β = 89.92
c = 189.253γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2008-04-04SINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 24-ID-C0.9795APS24-ID-C

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
12.65097.10.0860.0869.72.662935628782
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.62.6992.90.2952.42.55984

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 3GB52.613062878320296.820.1850.1850.1810.264RANDOM35.532
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]
-1.13-0.16-4.055.19
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.104
r_dihedral_angle_3_deg20.523
r_dihedral_angle_4_deg19.877
r_dihedral_angle_1_deg7.36
r_scangle_it3.693
r_scbond_it2.338
r_angle_refined_deg1.926
r_mcangle_it1.502
r_mcbond_it0.832
r_nbtor_refined0.324
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.104
r_dihedral_angle_3_deg20.523
r_dihedral_angle_4_deg19.877
r_dihedral_angle_1_deg7.36
r_scangle_it3.693
r_scbond_it2.338
r_angle_refined_deg1.926
r_mcangle_it1.502
r_mcbond_it0.832
r_nbtor_refined0.324
r_nbd_refined0.251
r_symmetry_vdw_refined0.206
r_xyhbond_nbd_refined0.179
r_chiral_restr0.137
r_symmetry_hbond_refined0.11
r_bond_refined_d0.019
r_gen_planes_refined0.008
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms14232
Nucleic Acid Atoms
Solvent Atoms300
Heterogen Atoms378

Software

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