X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 4.6
Temperature 293.0
Details 10% (v/v) PEG 400, 0.1M sodium acetate pH4.6, 0.13M CaCl2, Cryoprotected by increasing PEG 400 to 30%, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 142.71 α = 90
b = 168.95 β = 90
c = 131.07 γ = 90
Symmetry
Space Group C 2 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MAR CCD 165 mm -- 2010-03-19
Diffraction Radiation
Monochromator Protocol
Si 111 CHANNEL SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X4C 0.979 NSLS X4C

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
2.7 40 99.8 -- 0.135 -- 5.6 43603 43500 -- -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)
2.7 2.8 99.8 -- 0.539 3.1 5.4 4289

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 2.7 20.0 -- -- -- 41130 2176 98.11 -- 0.21572 0.21413 0.24539 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 2.7 2.759 -- 130 2390 0.321 0.37 -- 79.05
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 43.496
Anisotropic B[1][1] 2.83
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -1.25
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.58
RMS Deviations
Key Refinement Restraint Deviation
r_chiral_restr 0.117
r_gen_planes_refined 0.008
r_angle_refined_deg 1.768
r_scangle_it 5.29
r_scbond_it 2.983
r_mcangle_it 1.816
r_dihedral_angle_1_deg 18.922
r_mcbond_it 0.937
r_dihedral_angle_2_deg 35.032
r_dihedral_angle_4_deg 21.163
r_bond_refined_d 0.019
r_dihedral_angle_3_deg 16.535
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3274
Nucleic Acid Atoms 0
Heterogen Atoms 40
Solvent Atoms 301

Software

Software
Software Name Purpose
MAR345 data collection version: software
PHASER phasing
REFMAC refinement version: 5.5.0072
DENZO data reduction
SCALEPACK data scaling