X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1YH3 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP42980.1M sodium acetate pH4.0, 0.2M ammonium acetate, 3% isopropanol, 15% PEG 10000, vapor diffusion, hanging drop, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.2244.68

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 41.914α = 65.21
b = 50.847β = 83.6
c = 68.617γ = 82.52
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX-2252010-05-08MSINGLE WAVELENGTH
21
31
41
51
61
71
81
91
101
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL17U0.97908SSRFBL17U

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
12.045097.90.06911.13.531537
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)
12.042.1296.80.3843.43108

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 REPLACEMENTTHROUGHOUT1YH32.045031515158397.180.18510.18290.2273RANDOM38.506
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]
-0.42-0.28-0.67-0.520.750.53
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.145
r_dihedral_angle_4_deg14.892
r_dihedral_angle_3_deg13.155
r_dihedral_angle_1_deg5.305
r_scangle_it2.255
r_scbond_it1.429
r_angle_refined_deg1.088
r_angle_other_deg0.799
r_mcangle_it0.797
r_mcbond_it0.401
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.145
r_dihedral_angle_4_deg14.892
r_dihedral_angle_3_deg13.155
r_dihedral_angle_1_deg5.305
r_scangle_it2.255
r_scbond_it1.429
r_angle_refined_deg1.088
r_angle_other_deg0.799
r_mcangle_it0.797
r_mcbond_it0.401
r_mcbond_other0.096
r_chiral_restr0.067
r_bond_refined_d0.008
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4089
Nucleic Acid Atoms
Solvent Atoms237
Heterogen Atoms26

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction