X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 294.0
Details 1.25M Ammonium Sulfate, 11% (v/v) Glycerol, 0.1M Bis-Tris pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 94.28 α = 90
b = 96.22 β = 90
c = 210.24 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 RAYONIX MX300HE DCM with cryo-cooled 1st crystal sagittally bent 2nd crystal followed by vertically focusing mirror. 2011-05-26
Diffraction Radiation
Monochromator Protocol
double crystal monochromator (DCM) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON CLSI BEAMLINE 08B1-1 1.105 CLSI 08B1-1

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
2.12 50 98.4 0.109 -- -- 8.6 -- 63206 2.0 -3.0 --
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)
2.12 2.2 94.4 0.981 -- -- 5.2 --

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 2.5 48.6 -- -- 107698 59979 3180 94.1 -- 0.23189 0.2298 0.27068 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 2.498 2.563 -- 217 4406 0.288 0.358 -- 95.05
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 49.563
Anisotropic B[1][1] 4.01
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -1.38
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -2.63
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 0.611
r_scbond_it 0.366
r_mcangle_it 0.236
r_mcbond_it 0.122
r_gen_planes_other 0.001
r_gen_planes_refined 0.003
r_chiral_restr 0.048
r_dihedral_angle_4_deg 14.816
r_dihedral_angle_3_deg 13.168
r_dihedral_angle_2_deg 29.671
r_dihedral_angle_1_deg 4.442
r_angle_other_deg 0.71
r_angle_refined_deg 0.903
r_bond_other_d 0.001
r_bond_refined_d 0.005
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 13167
Nucleic Acid Atoms 0
Heterogen Atoms 282
Solvent Atoms 458

Software

Computing
Computing Package Purpose
MxDC Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL Data Reduction (data scaling)
PHASES Structure Solution
REFMAC 5.7.0029 Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.10 data extraction
REFMAC5 refinement
HKL data reduction