X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 8.1
Temperature 293.0
Details pH 8.1, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 63.91 α = 90
b = 215.47 β = 72
c = 64.01 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
-- -- -- 2003-04-05
-- -- -- 2003-09-04
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID14-4 -- ESRF ID14-4
SYNCHROTRON ESRF BEAMLINE BM30A -- ESRF BM30A

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
1.85 29.5 99.0 0.063 -- -- 2.0 -- 138110 -- 0.0 --
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)
1.85 2.0 92.1 0.262 -- 3.0 1.8 --

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 1.85 29.5 -- 0.0 -- 131161 6949 94.0 -- 0.213 0.211 0.261 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 1.85 1.93 -- 799 15191 0.237 0.311 -- 94.16
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 27.94
Anisotropic B[1][1] -0.96
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.2
Anisotropic B[2][2] 2.36
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.53
RMS Deviations
Key Refinement Restraint Deviation
r_xyhbond_nbd_refined 0.198
r_symmetry_hbond_refined 0.222
r_mcbond_it 1.485
r_dihedral_angle_4_deg 15.811
r_chiral_restr 0.087
r_symmetry_vdw_refined 0.225
r_nbd_refined 0.221
r_gen_planes_refined 0.005
r_metal_ion_refined 0.337
r_angle_refined_deg 1.293
r_scbond_it 3.168
r_dihedral_angle_1_deg 5.89
r_nbtor_refined 0.312
r_dihedral_angle_2_deg 36.225
r_mcangle_it 1.986
r_scangle_it 4.108
r_dihedral_angle_3_deg 16.068
r_bond_refined_d 0.011
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 13856
Nucleic Acid Atoms 0
Heterogen Atoms 43
Solvent Atoms 970

Software

Software
Software Name Purpose
REFMAC refinement version: 5.2.0005
PDB_EXTRACT data extraction version: 1.700
XDS data reduction
XDS data scaling
PHASER phasing