X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5.6
Temperature 298.0
Details 15% PEG 4K, 100 mM sodium citrate, 100 mM lithium acetate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 174.29 α = 90
b = 88.36 β = 106.8
c = 61.35 γ = 90
Symmetry
Space Group C 1 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 200
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 Crystal type: Si(111) Mirrors: Rh coated flat mirror 2006-07-15
Diffraction Radiation
Monochromator Protocol
Side scattering bent cube-root I-beam single crystal; asymmetric cut 4.965 degs SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL11-1 0.9795 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
2 20 97.9 -- 0.058 -- 4.0 -- 59119 0.0 -3.0 35.0
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)
2.0 2.07 95.6 -- 0.548 3.2 3.4 5746

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 20.0 -- -- 58980 55989 2991 100.0 0.20501 0.20501 0.20125 0.27725 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 2.051 -- 214 4056 0.293 0.359 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model ISOTROPIC + TLS REFINEMENT
Mean Isotropic B 41.559
Anisotropic B[1][1] -2.84
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -1.94
Anisotropic B[2][2] 1.8
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.08
RMS Deviations
Key Refinement Restraint Deviation
r_scbond_it 2.614
r_symmetry_vdw_refined 0.251
r_chiral_restr 0.127
r_bond_refined_d 0.023
r_scangle_it 3.652
r_xyhbond_nbd_refined 0.199
r_dihedral_angle_1_deg 6.362
r_dihedral_angle_3_deg 16.964
r_mcangle_it 1.443
r_dihedral_angle_2_deg 37.508
r_dihedral_angle_4_deg 19.793
r_gen_planes_refined 0.01
r_nbtor_refined 0.315
r_symmetry_hbond_refined 0.231
r_angle_refined_deg 1.914
r_mcbond_it 1.023
r_nbd_refined 0.228
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 6266
Nucleic Acid Atoms 0
Heterogen Atoms 51
Solvent Atoms 511

Software

Software
Software Name Purpose
REFMAC refinement version: 5.2.0019
Blu-Ice data collection
DENZO data reduction
SCALEPACK data scaling
AMoRE phasing
XFIT data reduction