X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7.5
Temperature 282.0
Details Protein solution was at 15 mg/mL containing 20 mM Tris (pH 7.5), 100 mM NaCl, 10 mM EDTA and 10 mM bME, 5 mM SAH, 5 mM phosphoethanolamine. Mother liqueur contained 0.04 M potassium phosphate (monobasic), 16% PEG 8,000 and 20% v/v glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 282K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 57.13 α = 107.18
b = 68.01 β = 96.3
c = 74.74 γ = 106.51
Symmetry
Space Group P 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD RAYONIX MX-300 -- 2012-06-03
Diffraction Radiation
Monochromator Protocol
C(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 21-ID-G -- APS 21-ID-G

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
1.45 30 96.5 -- 0.05 -- 4.3 -- 172409 -- 0.0 --
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)
1.45 1.5 93.3 0.634 -- -- 3.6 --

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 1.45 29.63 -- 0.0 178550 152982 7671 85.7 -- 0.172 0.17 0.194 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 1.45 1.49 -- 186 3471 0.221 0.263 -- 27.81
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 20.18
Anisotropic B[1][1] -0.01
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.0
Anisotropic B[2][3] 0.01
Anisotropic B[3][3] 0.01
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_4_deg 17.455
r_gen_planes_refined 0.006
r_angle_refined_deg 1.287
r_dihedral_angle_2_deg 34.602
r_chiral_restr 0.088
r_dihedral_angle_3_deg 13.391
r_bond_refined_d 0.008
r_dihedral_angle_1_deg 5.746
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 6914
Nucleic Acid Atoms 0
Heterogen Atoms 76
Solvent Atoms 1086

Software

Software
Software Name Purpose
SCALEPACK data scaling
REFMAC refinement
PDB_EXTRACT data extraction version: 3.11
HKL-3000 data reduction
PHASER phasing