X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 4
Details HANGING DROP WITH 5 MG/ML PROTEIN AND 18% (V/V) DIOXANE. RESERVOIR WITH 35% (V/V) DIOXANE. HAMPTON CRYSTAL SCREEN-2 NO.4, pH 4.00

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 108.02 α = 90
b = 108.02 β = 90
c = 57.17 γ = 90
Symmetry
Space Group P 4 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MARRESEARCH -- 1999-03-15
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE BW7B -- EMBL/DESY, HAMBURG BW7B

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
1.35 30.5 96.0 0.052 -- -- 3.7 -- 71387 -- -- 10.6
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)
1.35 1.4 95.0 0.38 -- 1.7 3.4 --

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 1.35 30.43 -- -- -- 69212 2175 95.8 -- 0.112 0.111 0.142 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 1.35 1.39 -- 148 4849 0.209 0.306 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 12.43
Anisotropic B[1][1] -0.27
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.27
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.53
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 5.99
r_scbond_it 4.896
r_mcangle_it 3.696
r_mcbond_it 2.842
r_nbd_refined 0.229
r_gen_planes_other 0.002
r_gen_planes_refined 0.004
r_chiral_restr 0.086
r_dihedral_angle_3_deg 15.776
r_dihedral_angle_1_deg 4.067
r_angle_other_deg 1.112
r_angle_refined_deg 1.252
r_bond_other_d 0.001
r_bond_refined_d 0.007
r_nbd_other 0.188
r_nbtor_other 0.229
r_xyhbond_nbd_refined 0.191
r_xyhbond_nbd_other 0.179
r_metal_ion_refined 0.101
r_symmetry_vdw_refined 0.278
r_symmetry_vdw_other 0.196
r_symmetry_hbond_refined 0.283
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2120
Nucleic Acid Atoms 0
Heterogen Atoms 47
Solvent Atoms 525

Software

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