X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 4.6
Temperature 300.0
Details The concentration of the protein was 20mg/ml. The precipitant solution in the reservoir was 0.1 M sodium acetate/acetic acid buffer of pH 4.6 to 5.0 containing 1.2 to 1.5M sodium chloride. The soaking solution was 0.1M sodium acetate/acetic acid buffer at pH 3.5 containing 1.4M NaCl, 25% v/v glycerol (as cryo-protectant) and 2.5M of guanidine hydrochloride

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 78.28 α = 90
b = 78.28 β = 90
c = 36.96 γ = 90
Symmetry
Space Group P 43 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD RIGAKU SATURN 944+ -- 2016-06-16
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU MICROMAX-007 HF 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
1.76 55.35 87.7 -- -- -- 1.9 -- 10506 -- -- 14.35
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)
1.76 1.818 -- -- -- -- -- --

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 1.76 55.35 -- -- -- 9979 527 87.66 -- 0.16886 0.16637 0.19823 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 1.755 1.801 -- 8 189 0.303 0.415 -- 22.8
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 14.736
Anisotropic B[1][1] 0.2
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.2
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.41
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_3_deg 13.012
r_bond_other_d 0.005
r_angle_other_deg 0.774
r_scbond_it 0.859
r_long_range_B_other 3.704
r_scbond_other 0.858
r_dihedral_angle_1_deg 5.737
r_angle_refined_deg 0.989
r_scangle_other 1.485
r_long_range_B_refined 4.045
r_dihedral_angle_2_deg 34.95
r_gen_planes_refined 0.003
r_mcangle_other 1.168
r_mcbond_it 0.69
r_mcbond_other 0.69
r_bond_refined_d 0.005
r_dihedral_angle_4_deg 16.743
r_chiral_restr 0.064
r_gen_planes_other 0.001
r_mcangle_it 1.168
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 990
Nucleic Acid Atoms 0
Heterogen Atoms 44
Solvent Atoms 165

Software

Software
Software Name Purpose
REFMAC refinement version: 5.8.0049
MOSFLM data reduction
Aimless data scaling
PHASER phasing