X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 293.0
Details PEG 600, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 191.98 α = 90
b = 56.62 β = 115.71
c = 105.52 γ = 90
Symmetry
Space Group C 1 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 225 mm CCD -- 2009-06-08
Diffraction Radiation
Monochromator Protocol
Si 111 CHANNEL SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.000 SPring-8 BL41XU

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
2.1 50 98.9 0.171 -- -- 5.1 -- 59046 -- -3.0 20.8
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)
2.1 2.18 94.8 0.497 -- -- 4.0 5628

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 2.1 50.0 -- 0.0 -- 58641 4149 97.19 -- 0.2015 0.1986 0.2395 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 2.097 2.151 -- 252 3134 0.224 0.277 -- 79.78
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 25.071
Anisotropic B[1][1] -2.02
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -1.04
Anisotropic B[2][2] 2.79
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.67
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_1_deg 5.819
r_dihedral_angle_2_deg 37.364
r_angle_refined_deg 1.579
r_dihedral_angle_4_deg 18.038
r_gen_planes_refined 0.008
r_bond_refined_d 0.013
r_chiral_restr 0.121
r_dihedral_angle_3_deg 18.354
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 6440
Nucleic Acid Atoms 0
Heterogen Atoms 239
Solvent Atoms 232

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
REFMAC refinement version: 5.6.0117
PDB_EXTRACT data extraction version: 3.11
BSS data collection
HKL-2000 data reduction
HKL-2000 data scaling
MOLREP phasing