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 Detector
Detector Diffraction Type Details Collection Date
-- -- -- --
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_scangle_it 5.613
r_scbond_it 3.882
r_mcangle_it 2.441
r_mcbond_it 1.684
r_nbd_refined 0.244
r_gen_planes_other 0.004
r_gen_planes_refined 0.011
r_chiral_restr 0.196
r_dihedral_angle_3_deg 14.623
r_dihedral_angle_1_deg 5.866
r_angle_other_deg 3.483
r_angle_refined_deg 1.816
r_bond_other_d 0.002
r_bond_refined_d 0.029
r_nbd_other 0.197
r_nbtor_other 0.371
r_xyhbond_nbd_refined 0.202
r_symmetry_vdw_refined 0.275
r_symmetry_vdw_other 0.265
r_symmetry_hbond_refined 0.194
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

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
CCP4 Structure Solution
REFMAC 5.0 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.0 refinement
CCP4 model building