X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 5.6
Temperature 293.0
Details PROTEIN SOLUTION: 10 MG/ML PROT., 25 0.17 M AMMONIUM ACETATE, 0.085 M TRI-SODIUM CITRATE (PH 5.6), 25.5 % W/V PEG 4000, 15 % GLYCEROL. V1/V2=1/1, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 90.96 α = 90
b = 162.7 β = 119.93
c = 90.94 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 315r -- 2013-11-20
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID23-1 0.97242 ESRF ID23-1

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
1.45 46 97.0 0.08 -- -- 2.6 -- 392121 -- -- --
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)
1.45 1.5 98.0 0.63 -- 2.0 -- --

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 1.45 45.48 -- -- -- 372619 19501 97.1 -- 0.143 0.142 0.165 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 1.45 1.49 -- 1412 27443 0.217 0.26 -- 96.7
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 17.74
Anisotropic B[1][1] -2.0
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.12
Anisotropic B[2][2] 6.23
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -4.23
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_4_deg 19.003
r_gen_planes_refined 0.01
r_mcbond_it 1.061
r_chiral_restr 0.113
r_mcangle_it 1.462
r_dihedral_angle_2_deg 34.465
r_dihedral_angle_1_deg 7.297
r_angle_refined_deg 1.717
r_bond_refined_d 0.013
r_dihedral_angle_3_deg 13.067
r_sphericity_bonded 5.898
r_scbond_it 1.508
r_long_range_B_refined 3.53
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 14539
Nucleic Acid Atoms 0
Heterogen Atoms 61
Solvent Atoms 1664

Software

Software
Software Name Purpose
XDS data reduction
XSCALE data scaling
REFMAC refinement version: 5.8.0073
MOLREP phasing