X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.5
Temperature 293.0
Details 50mM Tris-HCl, 0.1mM KCl, pH 7.5, temperature 293K, VAPOR DIFFUSION, HANGING DROP

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 109.08 α = 90
b = 109.08 β = 90
c = 176.52 γ = 90
Symmetry
Space Group P 43 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MAR scanner 345 mm plate -- 2011-04-04
Diffraction Radiation
Monochromator Protocol
Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRF BEAMLINE BL17U 0.9795 SSRF BL17U

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
2.25 50 99.9 0.074 -- -- 9.6 51206 51165 1.0 0.0 --
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)
2.25 2.33 100.0 0.692 -- -- 9.8 --

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 2.25 35.34 -- -- 51136 48252 2577 99.4 -- 0.21335 0.21162 0.24671 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 2.252 2.31 -- 169 3510 0.254 0.246 -- 99.11
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 45.436
Anisotropic B[1][1] 1.11
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 1.11
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -2.22
RMS Deviations
Key Refinement Restraint Deviation
r_angle_refined_deg 1.137
r_dihedral_angle_4_deg 15.534
r_dihedral_angle_3_deg 14.41
r_mcbond_it 0.671
r_scbond_it 1.951
r_bond_refined_d 0.012
r_dihedral_angle_1_deg 4.755
r_gen_planes_refined 0.005
r_dihedral_angle_2_deg 35.986
r_chiral_restr 0.086
r_scangle_it 3.226
r_mcangle_it 1.31
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4732
Nucleic Acid Atoms 0
Heterogen Atoms 4
Solvent Atoms 210

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
PHASER phasing version: 2.1.4
REFMAC refinement
PDB_EXTRACT data extraction version: 3.10
MAR345dtb data collection
HKL-2000 data reduction
HKL-2000 data scaling