X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 4.6
Details THE PROTEIN WAS CONCENTRATED IN WATER TO 7 MG/ML IT WAS INCUBATED 1H PRIOR CRYSTALLISATION WITH THE 5MM OF THE SUBSTRATE 16% PEG5KMME AND 200 MM CALCIUM ACETATE WERE USED AS PRECIPITANT AND 100 MM SODIUM ACETATE PH 4.6 AS BUFFER.

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 49.76 α = 90
b = 155.68 β = 118.42
c = 51.22 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC CCD -- 2000-11-15
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID14-4 -- ESRF ID14-4

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
1.75 40 97.5 0.041 -- -- 2.2 -- 69418 -- 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)
1.75 1.81 91.3 0.128 -- 6.0 2.0 --

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 1.75 38.92 -- -- -- 63815 3394 97.7 -- 0.135 0.133 0.168 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 1.75 1.79 -- 252 4393 0.147 0.2 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 9.06
Anisotropic B[1][1] 1.68
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.25
Anisotropic B[2][2] -1.26
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.17
RMS Deviations
Key Refinement Restraint Deviation
r_symmetry_vdw_refined 0.18
r_angle_other_deg 0.911
r_gen_planes_refined 0.009
r_gen_planes_other 0.006
r_nbtor_other 0.083
r_bond_other_d 0.002
r_mcangle_it 1.348
r_dihedral_angle_1_deg 5.904
r_nbd_other 0.255
r_symmetry_vdw_other 0.258
r_xyhbond_nbd_refined 0.131
r_symmetry_hbond_refined 0.154
r_mcbond_it 0.796
r_scangle_it 3.5
r_chiral_restr 0.1
r_scbond_it 2.331
r_angle_refined_deg 1.578
r_bond_refined_d 0.016
r_nbd_refined 0.221
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5630
Nucleic Acid Atoms 0
Heterogen Atoms 230
Solvent Atoms 715

Software

Software
Software Name Purpose
REFMAC refinement version: 5.1.24
DENZO data reduction
SCALEPACK data scaling
AMoRE phasing