X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 7.5
Temperature 277.0
Details CRYSTALS WERE PREPARED AT 277 K FROM THE DROPLET MIXTURE OF A 20 MG/ML PROTEIN SOLUTION CONTAINING 7 MM TRI-N-ACETYLCHITOTRIOSE (NAG3) AND 50 MM ACETATE BUFFER PH 4.2 WITH EQUAL VOLUME OF A RESERVOIR SOLUTION CONTAINING 2.0 M AMMONIUM FORMATE AND 100 MM N-(2-HYDROXYETHYL)PIPERAZINE-N'-(2-ETHANESULFONIC ACID) (HEPES) BUFFER PH 7.5. PRIOR TO THE DIFFRACTION DATA COLLECTION, THE CRYSTAL WAS SOAKED IN A CRYOPROTECTANT SOLUTION CONTAINING 30 % (W/V) POLYETHYLENE GLYCOL 20,000, 2.2 M AMMONIUM FORMATE, 100 MM HEPES BUFFER PH 7.5, AND 7 MM NAG3 FOR 2 MINUTES AT 277 K.

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 76.66 α = 90
b = 76.66 β = 90
c = 38.29 γ = 90
Symmetry
Space Group P 43 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU MIRRORS 1997-03
Diffraction Radiation
Monochromator Protocol
NI FILTER --
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RUH3R -- -- --

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
1.8 34.3 95.8 0.049 -- -- 11.0 -- 10515 -- 0.0 15.4
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)
1.8 1.86 64.9 0.147 -- 7.1 5.6 --

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 1.8 34.3 -- 0.0 -- 10515 992 95.8 -- 0.184 0.184 0.23 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 1.8 1.86 -- 75 673 0.233 0.268 0.031 69.4
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 14.7
RMS Deviations
Key Refinement Restraint Deviation
x_scangle_it 3.21
x_scbond_it 2.17
x_mcangle_it 1.9
x_mcbond_it 1.27
x_improper_angle_d 1.37
x_bond_d 0.01
x_angle_deg 1.29
x_dihedral_angle_d 23.1
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.2
Luzzati Sigma A (Observed) 0.18
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.23
Luzzati Sigma A (R-Free Set) 0.18
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1001
Nucleic Acid Atoms 0
Heterogen Atoms 43
Solvent Atoms 184

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
X-PLOR 3.843 Structure Solution
X-PLOR 3.843 Structure Refinement
Software
Software Name Purpose
X-PLOR version: 3.843 refinement
X-PLOR version: 3.843 model building
SCALEPACK data reduction
DENZO data collection