X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5.6
Temperature 293.0
Details Reservoir: 20% isopropanol, 25% PEG 4k, 0.1 M NaCitrate. Protein: 7-15 mg/ml, 10 mM HEPES, 20 mM NaCl, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 108.79 α = 90
b = 108.79 β = 90
c = 47.35 γ = 90
Symmetry
Space Group P 4

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARRESEARCH -- 2005-04-19
Diffraction Radiation
Monochromator Protocol
Si 220 SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 22-ID 0.99997 APS 22-ID

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
2.25 40 98.9 0.089 -- -- 3.1 26406 26406 1.0 1.0 34.6
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)
2.25 2.33 100.0 0.437 -- 2.93 3.0 --

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 2.25 40.0 -- 0.0 25130 25130 1276 98.93 0.17528 0.17528 0.17188 0.24447 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 2.25 2.308 -- 99 1828 0.185 0.274 -- 99.95
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 23.671
Anisotropic B[1][1] 0.62
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.62
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.25
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 3.607
r_scbond_it 2.42
r_mcangle_it 3.18
r_mcbond_it 2.078
r_nbd_refined 0.245
r_gen_planes_refined 0.009
r_chiral_restr 0.123
r_dihedral_angle_4_deg 16.385
r_dihedral_angle_3_deg 16.342
r_dihedral_angle_2_deg 33.967
r_dihedral_angle_1_deg 4.892
r_angle_refined_deg 1.977
r_bond_refined_d 0.023
r_nbtor_refined 0.329
r_xyhbond_nbd_refined 0.244
r_symmetry_vdw_refined 0.281
r_symmetry_hbond_refined 0.319
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4042
Nucleic Acid Atoms 0
Heterogen Atoms 20
Solvent Atoms 204

Software

Computing
Computing Package Purpose
SERGUI, MARCCD Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
MOLREP Structure Solution
REFMAC 5.2.0005 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.2.0005 refinement