X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6.25
Temperature 298.0
Details "Protein (20 MM HEPES, PH 7.3, 110 MM POTASSIUM ACETATE, 2MM MAGNESIUM ACET ATE, 20% GLYCEROL, 2MM DTT); Reservoir (0.2 M Sodiumchloride, 0.8M Sodiumcitrate, 0.1M BisTris pH 6.25 ); Cryo (2.5 M Sodiummalonate)">, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 126.58 α = 90
b = 162.15 β = 90
c = 68.5 γ = 90
Symmetry
Space Group P 21 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315r MIRRORS 2013-03-20
Diffraction Radiation
Monochromator Protocol
Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X29A 1.0750 NSLS X29A

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
2.7 40 99.9 0.102 -- -- 5.3 39520 39520 0.0 0.0 54.3
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)
2.7 2.81 99.7 1.295 -- 1.4 5.3 4389

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 2.7 40.0 -- 0.0 -- 39470 1977 99.79 -- 0.1912 0.1886 0.2384 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 2.7 2.77 2718 147 2718 0.35 0.384 -- 99.58
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 67.545
Anisotropic B[1][1] -4.24
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 3.52
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.72
RMS Deviations
Key Refinement Restraint Deviation
r_gen_planes_other 0.001
r_chiral_restr 0.079
r_angle_other_deg 0.825
r_dihedral_angle_3_deg 16.998
r_mcbond_other 4.261
r_mcangle_it 6.521
r_bond_other_d 0.002
r_mcbond_it 4.262
r_angle_refined_deg 1.44
r_dihedral_angle_4_deg 19.389
r_bond_refined_d 0.011
r_gen_planes_refined 0.007
r_dihedral_angle_2_deg 42.117
r_dihedral_angle_1_deg 6.008
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 6735
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 18

Software

Software
Software Name Purpose
REFMAC refinement version: 5.8.0049
PDB_EXTRACT data extraction version: 3.14
CBASS data collection
XDS data reduction
XDS data scaling
PHASER phasing