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 -- 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_scangle_it 3.5
r_scbond_it 2.331
r_mcangle_it 1.348
r_mcbond_it 0.796
r_nbd_refined 0.221
r_gen_planes_other 0.006
r_gen_planes_refined 0.009
r_chiral_restr 0.1
r_dihedral_angle_1_deg 5.904
r_angle_other_deg 0.911
r_angle_refined_deg 1.578
r_bond_other_d 0.002
r_bond_refined_d 0.016
r_nbd_other 0.255
r_nbtor_other 0.083
r_xyhbond_nbd_refined 0.131
r_symmetry_vdw_refined 0.18
r_symmetry_vdw_other 0.258
r_symmetry_hbond_refined 0.154
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

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
AMORE Structure Solution
REFMAC 5.1.24 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.1.24 refinement
AMORE model building