X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion
pH 7.5
Temperature 298.0
Details 15% PEG 4000, 300mM MgCl2, 100mM Tris, pH 7.5, vapor diffusion, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 75.36 α = 90
b = 78.16 β = 90
c = 93.77 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 300 mm CCD -- 2013-02-25
Diffraction Radiation
Monochromator Protocol
Si SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON CLSI BEAMLINE 08B1-1 0.97949 CLSI 08B1-1

Data Collection

Overall
Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot
1.3 50 99.4 0.041 -- -- 5.5 -- 135702 1.0 1.0 --
High Resolution Shell
Resolution (High) Resolution (Low) Percent Possible (All) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All)
1.3 1.35 100.0 0.568 -- -- 5.4 13514

Refinement

Statistics
Structure Solution Method Refinement High Resolution Refinement Low Resolution Cut-off Sigma (I) Cut-off Sigma (F) Number of Reflections (All) Number of Reflections (Observed) Number of Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work R-Free R-Free Selection Details
MOLECULAR REPLACEMENT 1.3 40.04 -- 0.0 -- 123935 6249 90.53 -- 0.1207 0.1194 0.1453 RANDOM
High Resolution Shell
Refinement method Shell Resolution (High) Shell Resolution (Low) # of Reflections (Observed) # of Reflections (R-Free) # of Reflections (R-Work) R-Factor (R-Work) R-Factor (R-Free) R-Factor (R-Free Error) Percent Reflections (Observed)
X Ray Diffraction 1.3 1.332 -- 168 2773 0.126 0.175 -- 29.59
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 24.2539
Anisotropic B[1][1] -0.24
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.15
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.39
RMS Deviations
Key Refinement Restraint Deviation
r_angle_refined_deg 1.442
r_angle_other_deg 0.764
r_rigid_bond_restr 2.84
r_sphericity_free 31.477
r_bond_other_d 0.001
r_dihedral_angle_1_deg 5.788
r_gen_planes_other 0.001
r_chiral_restr 0.083
r_dihedral_angle_2_deg 39.141
r_dihedral_angle_3_deg 12.653
r_bond_refined_d 0.011
r_sphericity_bonded 14.405
r_dihedral_angle_4_deg 15.633
r_gen_planes_refined 0.007
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3595
Nucleic Acid Atoms 0
Heterogen Atoms 25
Solvent Atoms 691

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
REFMAC refinement
PDB_EXTRACT data extraction version: 3.11
CLS data collection
REFMAC phasing version: 5.6.0117