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 = 76.19 α = 90
b = 77.93 β = 90
c = 93.68 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 -- 2011-04-14
Diffraction Radiation
Monochromator Protocol
Si SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON CLSI BEAMLINE 08ID-1 0.97949 CLSI 08ID-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
1.5 50 94.2 0.041 -- -- 4.5 -- 84356 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)
1.5 1.55 67.1 0.37 -- -- 2.4 5931

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 1.5 35.29 -- 0.0 -- 84137 4190 93.9 -- 0.1299 0.1281 0.1636 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 1.5 1.54 -- 208 3804 0.25 0.264 -- 62.38
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 24.3113
Anisotropic B[1][1] -0.13
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.13
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.0
RMS Deviations
Key Refinement Restraint Deviation
r_bond_refined_d 0.01
r_dihedral_angle_2_deg 39.328
r_sphericity_bonded 14.098
r_angle_other_deg 0.748
r_gen_planes_refined 0.006
r_angle_refined_deg 1.356
r_dihedral_angle_1_deg 5.584
r_chiral_restr 0.075
r_rigid_bond_restr 2.193
r_gen_planes_other 0.001
r_dihedral_angle_4_deg 14.668
r_sphericity_free 29.634
r_bond_other_d 0.001
r_dihedral_angle_3_deg 12.575
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3542
Nucleic Acid Atoms 0
Heterogen Atoms 18
Solvent Atoms 636

Software

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