X-RAY DIFFRACTION Experimental Data & Validation

X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8
Temperature 277.0
Details 22% MPD, 25 mM Potassium Phosphate, Calcium Chloride, pdTp, Soaked in higher % MPD before freezing, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 30.98 α = 90
b = 60.28 β = 93.43
c = 37.96 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 110
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD BRUKER APEX II multi-layer optics 2008-06-15
Diffraction Radiation
Monochromator Protocol
GE111 SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SEALED TUBE OTHER 1.5418 -- --

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
2.1 60.28 100.0 0.0816 0.0349 -- 15.45 8220 8216 0.0 0.0 38.6
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)
2.1 2.2 100.0 0.388 0.2114 4.49 11.86 1058

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 2.1 23.29 -- 0.0 8181 8181 803 99.78 0.215 0.215 0.209 0.278 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 2.1 2.154 585 60 521 0.303 0.365 -- 99.316
X Ray Diffraction 2.154 2.213 600 67 -- 0.247 0.35 -- 99.5
X Ray Diffraction 2.216 2.276 548 61 -- 0.244 0.327 -- 99.635
X Ray Diffraction 2.276 2.346 563 65 -- 0.243 0.354 -- 99.467
X Ray Diffraction 2.346 2.422 527 53 -- 0.249 0.384 -- 100.0
X Ray Diffraction 2.422 2.506 529 46 -- 0.249 0.338 -- 99.811
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 31.224
Anisotropic B[1][1] -0.05
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.01
Anisotropic B[2][2] 0.01
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.04
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_3_deg 17.072
r_gen_planes_refined 0.008
r_bond_refined_d 0.008
r_mcbond_it 0.934
r_chiral_restr 0.095
r_angle_refined_deg 1.216
r_dihedral_angle_2_deg 33.39
r_dihedral_angle_4_deg 14.772
r_scangle_it 3.985
r_dihedral_angle_1_deg 7.064
r_mcangle_it 1.683
r_scbond_it 2.636
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1034
Nucleic Acid Atoms 0
Heterogen Atoms 26
Solvent Atoms 45

Software

Software
Software Name Purpose
SAINT data scaling
PHASER phasing
REFMAC refinement version: 5.5.0036
PDB_EXTRACT data extraction version: 3.006
APEX data collection
SAINT data reduction