X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6
Temperature 293.0
Details Reservoir: 0.1M Ammonium Acetate, 0.1M Bis-Tris, 17% PEG 10000. Protein buffer and concentration: 5mM Sodium Acetate, pH 5.5, Cpr=5.25mg/ml. Ratio Protein: Reservoir=2:1. Cryocooled in mother liquor containing 20% ethylene glycol., VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 54.28 α = 76.97
b = 83.17 β = 86.6
c = 84.57 γ = 71.11
Symmetry
Space Group P 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 225 mm CCD Double crystal monochromator with 2 sets of Rh-soated silicon and glass mirrors 2011-06-01
Diffraction Radiation
Monochromator Protocol
Si(111) crystal SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON BESSY BEAMLINE 14.2 0.914 BESSY 14.2

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
1.95 50 78.4 0.037 -- -- 2.3 -- 78650 0.0 0.0 25.2
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)
1.95 1.98 42.1 0.296 -- 3.1 1.9 --

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 1.95 38.4 0.0 0.0 95142 71614 3756 75.27 0.20195 0.20195 0.19927 0.25245 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 1.945 1.996 -- 84 1585 0.247 0.285 -- 22.55
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 21.792
Anisotropic B[1][1] 0.0
Anisotropic B[1][2] 0.01
Anisotropic B[1][3] 0.01
Anisotropic B[2][2] 0.01
Anisotropic B[2][3] 0.01
Anisotropic B[3][3] -0.01
RMS Deviations
Key Refinement Restraint Deviation
r_xyhbond_nbd_refined 0.151
r_scbond_it 1.513
r_scangle_it 2.26
r_mcbond_it 0.565
r_symmetry_hbond_refined 0.227
r_dihedral_angle_2_deg 34.195
r_nbd_refined 0.205
r_dihedral_angle_4_deg 17.278
r_bond_refined_d 0.012
r_angle_refined_deg 1.303
r_nbtor_refined 0.306
r_dihedral_angle_3_deg 15.521
r_dihedral_angle_1_deg 6.062
r_chiral_restr 0.098
r_gen_planes_refined 0.005
r_symmetry_vdw_refined 0.181
r_mcangle_it 0.911
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 9797
Nucleic Acid Atoms 0
Heterogen Atoms 24
Solvent Atoms 519

Software

Software
Software Name Purpose
MarDB data collection
MOLREP phasing
REFMAC refinement version: 5.3.0037
HKL-3000 data reduction
HKL-3000 data scaling