X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 9
Details PROTEIN WAS CRYSTALLIZED FROM 50 MM TRIS-CL (PH 9-9.5), 10 MM NICL2, 12.5% GLYCEROL, AND 20% POLYETHYLENE GLYCOL 2000 MONOMETHYL ETHER

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 35.94 α = 90
b = 99.45 β = 100.57
c = 58.52 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 QUANTUM-4 2X2 ARRAY MIRRORS 2002-02-15
Diffraction Radiation
Monochromator Protocol
DOUBLE-CRYSTAL SI(111) MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ALS BEAMLINE 5.0.2 0.9786,0.9788 ALS 5.0.2

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
1.95 50 100.0 0.094 -- -- 7.5 -- 29176 -- 2.6 --
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)
1.95 1.98 100.0 0.896 -- 2.6 7.5 --

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
MAD 1.95 50.0 -- -- -- 27660 1477 99.6 -- -- 0.186 0.227 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 1.95 2.0 -- 108 1941 0.235 0.301 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 17.1
Anisotropic B[1][1] 1.09
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.51
Anisotropic B[2][2] -1.6
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.69
RMS Deviations
Key Refinement Restraint Deviation
r_mcbond_it 0.938
r_mcangle_it 1.737
r_gen_planes_refined 0.008
r_metal_ion_refined 0.047
r_symmetry_vdw_other 0.306
r_nbd_refined 0.213
r_scbond_it 3.506
r_nbtor_other 0.087
r_bond_refined_d 0.019
r_gen_planes_other 0.01
r_xyhbond_nbd_refined 0.194
r_scangle_it 5.155
r_dihedral_angle_1_deg 6.389
r_symmetry_hbond_refined 0.188
r_angle_other_deg 0.892
r_nbd_other 0.247
r_angle_refined_deg 1.673
r_chiral_restr 0.1
r_bond_other_d 0.002
r_symmetry_vdw_refined 0.267
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3239
Nucleic Acid Atoms 0
Heterogen Atoms 16
Solvent Atoms 123

Software

Software
Software Name Purpose
Quanta model building
SCALEPACK data scaling
CNS phasing
CCP4 phasing
SHARP phasing version: ARP/WARP
Quanta phasing
REFMAC refinement version: 5.1.24