X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 4.6
Temperature 297.0
Details 24 % PEG4000, 4 mM DTT, 0.15 mM Sodium citrate, pH4.6 Microseeding

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 104.31 α = 90
b = 111.11 β = 90
c = 122.52 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 QUANTUM 315r -- 2014-02-01
Diffraction Radiation
Monochromator Protocol
Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ALS BEAMLINE 5.0.3 0.98 ALS 5.0.3

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
2.35 50 99.6 -- 0.151 2.05 5.1 -- 49346 -- -- --
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)
2.35 2.39 99.9 -- -- -- 5.1 --

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
-- 2.51 39.74 -- -- -- 46618 2485 99.48 -- 0.20569 0.20419 0.23331 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 2.51 2.575 -- 173 3195 0.271 0.298 -- 94.08
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 28.501
Anisotropic B[1][1] 2.25
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -1.15
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.11
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_3_deg 14.78
r_mcangle_it 3.636
r_mcangle_other 3.636
r_angle_refined_deg 1.684
r_dihedral_angle_2_deg 35.1
r_mcbond_it 2.318
r_gen_planes_refined 0.008
r_long_range_B_refined 6.946
r_dihedral_angle_4_deg 18.093
r_scbond_other 3.18
r_scangle_other 4.985
r_mcbond_other 2.32
r_long_range_B_other 6.945
r_bond_refined_d 0.015
r_angle_other_deg 1.175
r_gen_planes_other 0.005
r_bond_other_d 0.007
r_chiral_restr 0.088
r_scbond_it 3.184
r_dihedral_angle_1_deg 6.568
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 8584
Nucleic Acid Atoms 0
Heterogen Atoms 109
Solvent Atoms 71

Software

Software
Software Name Purpose
REFMAC refinement version: 5.7.0032
HKL-2000 data reduction
HKL-2000 data scaling
PHENIX phasing