X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 4.4
Temperature 277.0
Details 2.0 M sodium formate, 100 mM sodium acetate pH 4.4

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 94.88 α = 90
b = 94.95 β = 90
c = 112.11 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 MARMOSAIC 300 mm CCD -- 2014-04-05
Diffraction Radiation
Monochromator Protocol
Double Si(111) crystal cryo-cooled SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 23-ID-B 1.03318 APS 23-ID-B

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
2.4 48.27 100.0 0.151 -- -- 7.4 -- 40325 -- -- --
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)
2.4 2.49 99.8 1.556 -- 1.5 7.5 4154

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 2.4 48.27 -- 0.0 -- 38215 2050 99.9 -- 0.1946 0.1918 0.247 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 2.399 2.462 -- 148 2741 0.312 0.322 -- 99.48
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 64.962
Anisotropic B[1][1] -3.25
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 1.96
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 1.29
RMS Deviations
Key Refinement Restraint Deviation
r_mcbond_other 4.356
r_dihedral_angle_1_deg 4.416
r_dihedral_angle_3_deg 15.482
r_bond_refined_d 0.014
r_dihedral_angle_4_deg 15.87
r_angle_other_deg 3.701
r_mcangle_it 6.339
r_chiral_restr 0.091
r_gen_planes_refined 0.006
r_angle_refined_deg 1.482
r_bond_other_d 0.0
r_gen_planes_other 0.009
r_mcbond_it 4.359
r_dihedral_angle_2_deg 41.388
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5280
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 223

Software

Software
Software Name Purpose
REFMAC refinement version: 5.8.0073
MOSFLM data reduction
Aimless data scaling version: 0.1.27
PHASER phasing version: 2.5.7
PDB_EXTRACT data extraction version: 3.15
XDS data reduction