X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3GNNpdb deposition 3GNN modified with CCP4 program CHAINSAW

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP290MD PACT SCREEN E6: 20% PEG 3350, 200MM NA-FORMATE; EHCHA.01074.A AT 29MG/ML, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 290K
Crystal Properties
Matthews coefficientSolvent content
2.3146.71

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 60.53α = 113.01
b = 77.32β = 91.82
c = 78.32γ = 111.68
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210r2009-11-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.10.9774ALS5.0.1

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
12.055096.60.08710.272.37474772223-324.47
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)
12.052.195.40.422.42.35510

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)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 deposition 3GNN modified with CCP4 program CHAINSAW2.05507474772216364096.80.1770.1770.1740.226RANDOM9.69
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]
0.28-0.2-0.05-0.43-0.26-0.21
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.917
r_dihedral_angle_4_deg19.633
r_dihedral_angle_3_deg13.669
r_dihedral_angle_1_deg6.009
r_scangle_it3.503
r_scbond_it2.193
r_angle_refined_deg1.454
r_mcangle_it1.342
r_angle_other_deg0.964
r_mcbond_it0.732
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.917
r_dihedral_angle_4_deg19.633
r_dihedral_angle_3_deg13.669
r_dihedral_angle_1_deg6.009
r_scangle_it3.503
r_scbond_it2.193
r_angle_refined_deg1.454
r_mcangle_it1.342
r_angle_other_deg0.964
r_mcbond_it0.732
r_mcbond_other0.186
r_chiral_restr0.093
r_bond_refined_d0.015
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8303
Nucleic Acid Atoms
Solvent Atoms853
Heterogen Atoms28

Software

Software
Software NamePurpose
BOSdata collection
PHASERphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling