X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 291.0
Details 1.35 M ammonium sulfate, 25% (v/v) glycerol, 4.8% (v/v) 1,6-hexanediol, 50 mM Mes-NaOH, 1mM EDTA, pH 6.5, vapor diffusion, hanging drop, temperature 291K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 159.76 α = 90
b = 159.76 β = 90
c = 124.14 γ = 90
Symmetry
Space Group P 41 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
AREA DETECTOR ADSC -- 2010-06-08
Diffraction Radiation
Monochromator Protocol
Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.98011 SOLEIL PROXIMA 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
2.65 38.02 99.3 -- 0.097 -- 3.7 -- 46986 -3.0 -3.0 --
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)
2.65 2.79 99.2 0.856 0.856 1.6 3.6 6741

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 2.65 38.02 -- 0.0 -- 46802 2359 98.88 0.21 0.2064 0.2052 0.2282 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 2.646 2.715 -- 188 3203 0.364 0.426 -- 98.78
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 55.6999
Anisotropic B[1][1] 1.22
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 1.22
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -2.44
RMS Deviations
Key Refinement Restraint Deviation
r_scbond_it 1.744
r_mcangle_it 1.361
r_dihedral_angle_3_deg 15.971
r_gen_planes_refined 0.007
r_scangle_it 2.988
r_chiral_restr 0.088
r_dihedral_angle_2_deg 33.509
r_dihedral_angle_4_deg 17.239
r_angle_refined_deg 1.556
r_mcbond_it 0.709
r_dihedral_angle_1_deg 5.982
r_bond_refined_d 0.012
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4362
Nucleic Acid Atoms 732
Heterogen Atoms 71
Solvent Atoms 234

Software

Software
Software Name Purpose
MOSFLM data reduction
SCALA data scaling version: 3.3.16
PHASER phasing
REFMAC refinement
PDB_EXTRACT data extraction version: 3.10
ADSC data collection version: Quantum