X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 293.0
Details 100mM MES, 20-30% PEG 4000, 50mM n-BOG, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 68.37 α = 90
b = 69.84 β = 90
c = 74.7 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 90
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARRESEARCH Dynamically bendable mirror 2008-09-01
Diffraction Radiation
Monochromator Protocol
Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SLS BEAMLINE X10SA 0.976416 SLS X10SA

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 40 98.3 0.044 -- -- 4.11 24803 24384 -- -3.0 36.194
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)
2.0 2.1 97.8 0.381 -- 4.5 4.18 3310

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 2.0 40.0 -- 0.0 24803 24381 853 100.0 -- 0.22 0.217 0.298 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 2.0 2.052 -- 62 1706 0.248 0.282 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 31.905
Anisotropic B[1][1] 0.81
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.88
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.07
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_4_deg 16.598
r_dihedral_angle_2_deg 36.306
r_angle_refined_deg 1.484
r_nbtor_refined 0.309
r_dihedral_angle_1_deg 5.446
r_mcangle_it 1.685
r_chiral_restr 0.105
r_dihedral_angle_3_deg 14.974
r_mcbond_it 1.018
r_nbd_refined 0.214
r_symmetry_hbond_refined 0.237
r_xyhbond_nbd_refined 0.183
r_gen_planes_refined 0.006
r_scbond_it 2.332
r_scangle_it 3.618
r_bond_refined_d 0.014
r_symmetry_vdw_refined 0.151
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2694
Nucleic Acid Atoms 0
Heterogen Atoms 48
Solvent Atoms 173

Software

Software
Software Name Purpose
XSCALE data scaling
PHASER phasing version: 1.3.1
REFMAC refinement
PDB_EXTRACT data extraction version: 3.005
XDS data scaling
XDS data reduction