X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.3
Temperature 281.0
Details protein solution: TRIS, potassium chloride, DTT, plus precipitant; precipitant: PEG 3350, sodium chloride, sodium citrate, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 281K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 52.2 α = 90
b = 85.8 β = 81.8
c = 103.9 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 277
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MARRESEARCH -- 1993-12-01
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON MPG/DESY, HAMBURG BEAMLINE BW6 -- MPG/DESY, HAMBURG BW6

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
1.75 50 90.5 0.052 -- -- 2.4 -- 196672 -- 0.0 19.9
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)
1.75 1.84 62.7 0.151 -- -- 1.4 8118

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
-- 1.75 10.0 0.0 0.0 -- 80753 4066 89.7 -- -- 0.182 0.215 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 1.75 1.86 -- 433 8162 0.257 0.254 0.012 56.9
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 28.7
Anisotropic B[1][1] 0.84
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.53
Anisotropic B[2][2] -0.58
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.26
RMS Deviations
Key Refinement Restraint Deviation
c_scangle_it 16.25
c_scbond_it 24.2
c_mcangle_it 2.18
c_mcbond_it 1.3
c_improper_angle_d 1.53
c_dihedral_angle_d 22.6
c_angle_deg 1.8
c_bond_d 0.007
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.2
Luzzati Sigma A (Observed) 0.19
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.22
Luzzati Sigma A (R-Free Set) 0.16
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 6316
Nucleic Acid Atoms 0
Heterogen Atoms 283
Solvent Atoms 581

Software

Computing
Computing Package Purpose
MOSFLM Data Reduction (intensity integration)
CCP4 (AGROVATA, ROTAVATA) Data Reduction (data scaling)
MLPHARE Structure Solution
X-PLOR Structure Refinement
Software
Software Name Purpose
X-PLOR refinement
MLPHARE model building
ROTAVATA-AGRAVATA data reduction
MOSFLM data collection