X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
Temperature 277.0
Details 0.2M magnesium nitrate, 20.0% polyethylene glycol 3350, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 50.15 α = 90
b = 98.17 β = 107.2
c = 68.93 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 KOHZU: Double Crystal Si(111) 2012-09-20
Diffraction Radiation
Monochromator Protocol
Double Crystal Si(111) MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ALS BEAMLINE 8.2.2 0.918401,0.979338,0.979111 ALS 8.2.2

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
1.91 29.3 96.2 0.051 -- -- -- -- 48771 -- -3.0 26.14
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)
1.91 1.98 95.4 0.564 -- 1.5 -- --

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 1.91 29.304 -- 0.0 -- 48740 2471 98.58 -- 0.1824 0.1798 0.2324 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 1.91 1.96 -- 172 3390 0.266 0.299 -- 97.56
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 36.0527
Anisotropic B[1][1] 0.22
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -0.35
Anisotropic B[2][2] 1.4
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.27
RMS Deviations
Key Refinement Restraint Deviation
r_mcangle_it 3.201
r_mcbond_other 2.249
r_bond_refined_d 0.008
r_bond_other_d 0.001
r_angle_refined_deg 1.181
r_angle_other_deg 0.671
r_dihedral_angle_1_deg 5.353
r_dihedral_angle_2_deg 35.96
r_dihedral_angle_3_deg 12.787
r_dihedral_angle_4_deg 19.036
r_chiral_restr 0.044
r_gen_planes_refined 0.005
r_gen_planes_other 0.001
r_mcbond_it 2.249
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4980
Nucleic Acid Atoms 0
Heterogen Atoms 87
Solvent Atoms 309

Software

Computing
Computing Package Purpose
XDS Data Reduction (intensity integration)
XSCALE Data Reduction (data scaling)
SHELXD,SHARP Structure Solution
REFMAC 5.7.0032 Structure Refinement
Software
Software Name Purpose
REFMAC5 version: 5.7.0032 refinement
Xscale version: March 15, 2012 data processing
SHARP phasing
SHELX phasing
pdb_extract version: 3.10 data extraction
MOLPROBITY version: 3beta29 validation