X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 5.8
Details 22.5% PEG 3350, 0.18 M AMMONIUM SULFATE, 0.12 M SODIUM THIOCYANATE, 0.09 M BIS-TRIS PH 5.5, 0.01 M TRIS PH 8.5 (FINAL MEASURED PH=5.82). THE PROTEIN WAS AT 2 MM (47 MG/ML), WITH 4 MM BENZYLAMINE AND 10 MM CALCIUM CHLORIDE ADDED TO STABILIZE IT. THE CRYSTALLIZATIONS WERE SET UP WITH A PHOENITO PROTOCOL (NEWMAN ET AL. 2008), WHERE A PHOENIX ROBOT (ART ROBBINS INSTRUMENTS, SUNNYSIDE, CA) WAS USED TO DISPENSE THE PROTEIN INTO AN SD2 CRYSTALLIZATION PLATE (PRE-FILLED WITH 50 ML RESERVOIR SOLUTION) AND A MOSQUITO ROBOT (TTP LABTECH, MELBOURN, UK) WAS USED TO DISPENSE THE RESERVOIR SOLUTION AND SEED STOCK OVER THE PROTEIN DROPLET.

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 54.08 α = 90
b = 58.35 β = 90
c = 66.89 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC CCD -- 2009-12-04
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX1 -- Australian Synchrotron MX1

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
1.23 44 97.5 0.06 -- -- 7.1 -- 60293 -- 1.0 --
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)
1.23 1.3 88.5 0.35 -- 4.9 6.0 --

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 1.25 43.97 -- -- -- 55351 2962 98.42 -- 0.14629 0.1453 0.16471 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 1.25 1.282 -- 190 3667 0.196 0.201 -- 92.96
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 9.427
Anisotropic B[1][1] 0.11
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.07
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.04
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_2_deg 40.481
r_gen_planes_refined 0.015
r_chiral_restr 0.158
r_dihedral_angle_3_deg 11.824
r_dihedral_angle_4_deg 22.943
r_angle_refined_deg 2.577
r_bond_refined_d 0.028
r_dihedral_angle_1_deg 7.151
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1629
Nucleic Acid Atoms 0
Heterogen Atoms 41
Solvent Atoms 299

Software

Software
Software Name Purpose
REFMAC refinement version: 5.6.0117
XDS data reduction
SCALA data scaling
PHASER phasing