X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7
Temperature 277.0
Details NANODROP, 0.25M Sodium chloride, 33.0% 2-methyl-2,4-pentanediol, 0.1M Tris-HCl pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 40.93 α = 90
b = 69.79 β = 90
c = 150.52 γ = 90
Symmetry
Space Group C 2 2 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 325 mm CCD Flat mirror (vertical focusing) 2007-01-06
Diffraction Radiation
Monochromator Protocol
Single crystal Si(111) bent (horizontal focusing) MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL11-1 0.91837, 0.97941, 0.97917 SSRL BL11-1

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
1.6 28.88 99.3 0.045 -- -- 7.2 -- 28987 -- -- 22.8
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)
1.6 1.66 97.3 0.675 -- 2.1 -- --

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
MAD 1.6 28.88 -- 0.0 -- 28943 1475 99.53 -- 0.18374 0.1822 0.21269 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 1.6 1.64 -- 92 1987 0.244 0.297 -- 97.33
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 15.049
Anisotropic B[1][1] 0.29
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 1.37
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.66
RMS Deviations
Key Refinement Restraint Deviation
r_angle_other_deg 0.966
r_bond_other_d 0.002
r_mcbond_it 2.3
r_nbtor_other 0.089
r_angle_refined_deg 1.748
r_mcangle_it 3.137
r_scbond_it 5.047
r_nbtor_refined 0.169
r_dihedral_angle_1_deg 8.183
r_gen_planes_refined 0.006
r_nbd_refined 0.217
r_scangle_it 7.412
r_xyhbond_nbd_refined 0.176
r_mcbond_other 0.739
r_dihedral_angle_4_deg 21.374
r_symmetry_vdw_refined 0.283
r_gen_planes_other 0.002
r_symmetry_vdw_other 0.292
r_bond_refined_d 0.016
r_nbd_other 0.203
r_chiral_restr 0.093
r_symmetry_hbond_refined 0.132
r_dihedral_angle_3_deg 14.455
r_xyhbond_nbd_other 0.002
r_dihedral_angle_2_deg 32.489
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1674
Nucleic Acid Atoms 0
Heterogen Atoms 6
Solvent Atoms 135

Software

Software
Software Name Purpose
MolProbity model building version: 3beta29
REFMAC refinement version: 5.2.0019
XSCALE data scaling
PDB_EXTRACT data extraction version: 2.000
MAR345 data collection version: CCD
XDS data reduction
SHARP phasing