X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Microseeding and Macroseeding Used to Increase Crystal Size
pH 8.5
Details PROTEIN WAS CRYSTALLIZED FROM 21% MME-PEG 5000, 0.2M TAPS/ KOH, PH 8.5, 2MM DITHIONITE. THEN MICROSEEDING AND MACROSEEDING USED TO INCREASE CRYSTAL SIZE, microseeding and macroseeding used to increase crystal size

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 62.8 α = 90
b = 62.8 β = 90
c = 320.9 γ = 90
Symmetry
Space Group P 43 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 287
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IIC 0.3 MM COLLIMATOR 1994-10
Diffraction Radiation
Monochromator Protocol
GRAPHITE(002) --
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RUH2R -- -- --

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
2.9 40 95.9 0.091 0.091 -- 5.9 -- 14645 -- 1.9 61.7
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)
2.9 2.97 76.3 0.37 0.37 1.9 4.5 --

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 2.9 40.0 -- 0.0 -- 14598 1485 95.9 -- 0.185 0.185 0.232 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 2.9 3.03 -- 137 1232 0.294 0.354 0.03 76.3
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model ONE B FOR MAIN CHAIN ATOM B FOR SIDE CHAIN ATOMS
Mean Isotropic B 50.3
Anisotropic B[1][1] -1.2
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -1.2
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 2.83
RMS Deviations
Key Refinement Restraint Deviation
x_improper_angle_d 1.1
x_bond_d 0.006
x_angle_deg 1.2
x_dihedral_angle_d 19.5
Coordinate Error
Parameter Value
Luzzati Sigma A (Observed) 0.35
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4234
Nucleic Acid Atoms 0
Heterogen Atoms 180
Solvent Atoms 0

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
CCP4 (AGROVATA, ROTAVATA) Data Reduction (data scaling)
AMORE, TFFC Structure Solution
X-PLOR 3.851 Structure Refinement
Software
Software Name Purpose
X-PLOR version: 3.851 refinement
TFFC model building
AMORE model building