X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6.5
Temperature 277.0
Details 0.2000M NaOAc, 30.0000% PEG-8000, 0.1M Cacodylate pH 6.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 54.22 α = 90
b = 76.98 β = 90
c = 132.8 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) 2009-03-27
Diffraction Radiation
Monochromator Protocol
Single crystal Si(111) bent monochromator (horizontal focusing) MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL11-1 0.91837,0.97993,0.97920 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
1.35 29.05 100.0 0.085 0.085 -- 3.6 -- 61313 -- -- 10.639
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)
1.35 1.39 100.0 0.59 0.59 1.9 3.1 4503

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 1.35 29.05 -- 0.0 -- 61269 3109 99.96 -- 0.151 0.15 0.172 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 1.35 1.385 -- 242 4253 0.264 0.262 -- 99.8
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 10.685
Anisotropic B[1][1] -0.09
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.17
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.08
RMS Deviations
Key Refinement Restraint Deviation
r_bond_other_d 0.003
r_mcbond_other 0.236
r_gen_planes_other 0.002
r_bond_refined_d 0.017
r_angle_refined_deg 1.71
r_dihedral_angle_1_deg 4.476
r_dihedral_angle_3_deg 10.233
r_angle_other_deg 1.199
r_dihedral_angle_2_deg 34.468
r_chiral_restr 0.098
r_scangle_it 3.598
r_dihedral_angle_4_deg 18.009
r_gen_planes_refined 0.008
r_mcbond_it 0.809
r_mcangle_it 1.386
r_scbond_it 2.287
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2218
Nucleic Acid Atoms 0
Heterogen Atoms 87
Solvent Atoms 356

Software

Software
Software Name Purpose
REFMAC refinement version: 5.5.0053
PHENIX refinement
SHELX phasing
MolProbity model building version: 3beta29
SCALA data scaling version: 3.2.5
PDB_EXTRACT data extraction version: 3.006
MOSFLM data reduction
SHELXD phasing
autoSHARP phasing