X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8
Temperature 293.0
Details 12% PEG3000, 150 mM Li2SO4, 0.1 M imidazole, 2% ethanol, 10% glycerol, 20 mM MgCl2, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 48.58 α = 90
b = 70.93 β = 99.4
c = 82.01 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 225 mm CCD -- 2008-06-17
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SLS BEAMLINE X06DA 0.97 SLS X06DA

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
2.07 53.38 99.8 0.123 0.122 -- 4.4 148474 33607 -- 4.0 --
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)
2.07 2.18 100.0 0.499 -- 4.0 -- --

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 2.07 53.38 -- -- 33657 31727 1693 99.34 -- 0.19022 0.18705 0.24987 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 2.07 2.124 -- 134 2342 0.23 0.324 -- 99.88
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 26.386
Anisotropic B[1][1] 0.82
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -0.26
Anisotropic B[2][2] 1.26
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -2.16
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 4.663
r_dihedral_angle_3_deg 16.724
r_mcangle_it 1.861
r_angle_refined_deg 1.996
r_dihedral_angle_4_deg 18.096
r_mcbond_it 1.113
r_bond_refined_d 0.024
r_chiral_restr 0.127
r_gen_planes_refined 0.01
r_dihedral_angle_1_deg 6.787
r_scbond_it 3.087
r_dihedral_angle_2_deg 38.74
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4174
Nucleic Acid Atoms 0
Heterogen Atoms 75
Solvent Atoms 430

Software

Software
Software Name Purpose
DNA data collection
AMoRE phasing
REFMAC refinement version: 5.5.0102
MOSFLM data reduction
SCALA data scaling