X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7.5
Temperature 293.0
Details Starting protein solution was 5.5 mg/ml protein in 25 mM sodium carbonate buffer-pH 10.5. The reservoir solution was 500 ul of 2.0 M sodium chloride and 50 mM HEPES-pH 7.5 buffer. Bipyramidal crystals resulted from 2 ul drops, using 0.7 ul protein solution and 1.3 ul well solution.

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 55.57 α = 90
b = 55.57 β = 90
c = 208.96 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 MAR scanner 300 mm plate 115 data frames were collected using 3 second exposures, with an oscillation angle of 1 degree, and a crystal-to-detector distance of 200 mm. 2007-12-12
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 21-ID-D 1.000 APS 21-ID-D

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
2.27 53.7 95.9 0.094 -- -- 4.7 15236 15236 -- -- --
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)
2.27 2.35 96.4 0.381 -- 1.75 4.9 --

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
MAD 2.276 53.7 -- -- -- 14531 766 96.06 -- 0.23813 0.23523 0.29458 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 2.276 2.335 -- 65 1037 0.262 0.399 -- 95.25
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 41.305
Anisotropic B[1][1] 1.24
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 1.24
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -2.49
RMS Deviations
Key Refinement Restraint Deviation
r_gen_planes_refined 0.009
r_dihedral_angle_1_deg 7.883
r_scbond_it 3.001
r_dihedral_angle_3_deg 21.268
r_dihedral_angle_4_deg 21.028
r_chiral_restr 0.126
r_bond_refined_d 0.019
r_dihedral_angle_2_deg 43.353
r_angle_refined_deg 1.798
r_mcbond_it 1.047
r_scangle_it 4.674
r_mcangle_it 1.917
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2390
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 47

Software

Software
Software Name Purpose
REFMAC refinement version: 5.5.0102
HKL-2000 data reduction
HKL-2000 data scaling
SOLVE phasing version: 2.08