X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 7
Details TAKE 2 - 10 MG/ML PROTEIN IN 20MM MOPS, 50MM NACL, 2% TREHALOSE, PH 7.5. ADD EQUAL VOLUME OF 70% MPD, 0.1M PHOSPHATE BUFFER PH 7.0 WITH 10MG/ML XYLOBIOSE IN A HANGING DROP EXPERIMENT AT 4 DEGREES CENTIGRADE.

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 50.97 α = 90
b = 90.73 β = 90
c = 97.58 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ELETTRA BEAMLINE 5.2R -- ELETTRA 5.2R

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
1.2 20 99.4 0.032 -- -- 5.0 -- 141707 -- 2.0 --
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)
1.2 1.22 91.9 0.235 -- 3.69 2.5 --

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 1.2 65.94 -- -- -- 133682 7056 99.3 -- 0.108 0.107 0.13 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 1.2 1.23 -- 482 9160 0.186 0.199 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 10.66
Anisotropic B[1][1] -0.22
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.36
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.14
RMS Deviations
Key Refinement Restraint Deviation
r_nbd_other 0.197
r_mcbond_it 1.684
r_symmetry_hbond_refined 0.194
r_angle_refined_deg 1.816
r_xyhbond_nbd_refined 0.202
r_scbond_it 3.882
r_nbtor_other 0.371
r_bond_other_d 0.002
r_dihedral_angle_1_deg 5.866
r_bond_refined_d 0.029
r_scangle_it 5.613
r_mcangle_it 2.441
r_gen_planes_other 0.004
r_angle_other_deg 3.483
r_dihedral_angle_3_deg 14.623
r_gen_planes_refined 0.011
r_nbd_refined 0.244
r_symmetry_vdw_refined 0.275
r_chiral_restr 0.196
r_symmetry_vdw_other 0.265
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3203
Nucleic Acid Atoms 0
Heterogen Atoms 20
Solvent Atoms 390

Software

Software
Software Name Purpose
REFMAC refinement version: 5.0
DENZO data reduction
SCALEPACK data scaling
CCP4 phasing