X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8.5
Temperature 278.0
Details 23 % (w/v) PEG 3350, 50 mM Tris/HCl pH 8.5, 100 mM MgCl2, 10% (v/v) glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 278K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 127.21 α = 84.04
b = 33.65 β = 81.55
c = 47.99 γ = 89.23
Symmetry
Space Group P 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD BRANDEIS -- 2000-04-16
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X12C -- NSLS X12C

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
2.5 50 94.1 0.043 -- -- 3.0 25209 25209 -10.0 -10.0 43.2
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)
2.5 2.59 75.4 0.142 -- -- 2.0 2031

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 2.51 40.74 0.0 0.0 26797 24505 2418 91.1 0.2352 0.231 0.231 0.265 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 2.5 2.66 -- 305 2753 0.307 0.325 0.019 67.1
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 44.1
Anisotropic B[1][1] -14.57
Anisotropic B[1][2] -1.26
Anisotropic B[1][3] -0.18
Anisotropic B[2][2] 10.92
Anisotropic B[2][3] -10.6
Anisotropic B[3][3] 3.65
RMS Deviations
Key Refinement Restraint Deviation
c_mcbond_it 1.06
c_scangle_it 2.91
c_angle_deg 1.1
c_mcangle_it 1.74
c_bond_d 0.005
c_dihedral_angle_d 18.1
c_scbond_it 1.92
c_improper_angle_d 0.67
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.35
Luzzati Sigma A (Observed) 0.37
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.4
Luzzati Sigma A (R-Free Set) 0.41
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4846
Nucleic Acid Atoms 0
Heterogen Atoms 1
Solvent Atoms 112

Software

Software
Software Name Purpose
AMoRE phasing
CNS refinement version: 1.0
DENZO data reduction
SCALEPACK data scaling