X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 4.6
Temperature 291.0
Details 10 MG/ML OF LYSINE MODIFIED (ETHYLATED) PROTEIN IN 30 MM TRIS PH 8.0, 500 MM NACL, 1 MM GLEEVEC, MIXED 1:1 WITH 200 MM AMMONIUM ACETATE, 100 MM SODIUM ACETATE TRIHYDRATE PH 4.6 AND 30% PEG 4000, HANGING DROP, MICRO SEEDING WITH INITIAL CRYSTALS FROM A 96 WELL PLATE SCREEN, INITIAL CRYSTALS GREW ON A DUST PARTICLE, 18C

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 71.03 α = 90
b = 56.87 β = 116.62
c = 76.12 γ = 90
Symmetry
Space Group I 1 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 -- 2014-01-29
Diffraction Radiation
Monochromator Protocol
DOUBLE CRYSTAL, SI(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ALS BEAMLINE 8.2.2 -- 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
2.05 42.36 93.1 0.04 -- -- 2.5 -- 15954 -- 2.0 --
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)
2.05 2.11 96.8 0.41 -- 2.0 2.5 --

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
MOLECULAR REPLACEMENT 2.05 62.43 -- -- -- 14124 886 87.13 -- 0.19044 0.18728 0.24159 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 2.049 2.102 -- 54 1137 0.305 0.373 -- 91.33
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 59.54
Anisotropic B[1][1] 0.15
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 2.67
Anisotropic B[2][2] -3.16
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.22
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_3_deg 16.286
r_dihedral_angle_4_deg 12.224
r_mcangle_it 5.207
r_angle_refined_deg 1.42
r_angle_other_deg 0.974
r_gen_planes_refined 0.007
r_gen_planes_other 0.008
r_bond_refined_d 0.01
r_mcbond_other 3.571
r_mcbond_it 3.585
r_scbond_it 4.219
r_bond_other_d 0.002
r_dihedral_angle_2_deg 40.719
r_dihedral_angle_1_deg 6.263
r_chiral_restr 0.081
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1968
Nucleic Acid Atoms 0
Heterogen Atoms 37
Solvent Atoms 56

Software

Software
Software Name Purpose
REFMAC refinement version: 5.8.0049
XDS data reduction
Aimless data scaling
MOLREP phasing version: AUTO MR