X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.2
Temperature 277.0
Details MOPS BUFFER, PEG MME 2K, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 51.33 α = 72.54
b = 64.55 β = 73.29
c = 64.35 γ = 73.58
Symmetry
Space Group P 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 120
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MACSCIENCE mirrors 2000-01-01
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE ENRAF-NONIUS FR591 1.5418 -- --

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
2.15 30 95.3 -- 0.068 -- 1.74 40070 38187 -- -3.0 34.5
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)
2.15 2.19 87.5 -- 0.229 2.7 -- --

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 2.15 30.15 -- -- -- 36555 1632 91.2 -- 0.18376 0.18215 0.21646 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 2.15 -- -- -- -- 0.222 0.286 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 22.081
Anisotropic B[1][1] -0.47
Anisotropic B[1][2] -0.3
Anisotropic B[1][3] 0.05
Anisotropic B[2][2] -0.04
Anisotropic B[2][3] -0.04
Anisotropic B[3][3] 0.67
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 3.429
r_scbond_it 2.15
r_mcangle_it 1.347
r_nbd_refined 0.238
r_gen_planes_other 0.004
r_gen_planes_refined 0.007
r_chiral_restr 0.097
r_dihedral_angle_2_deg 18.201
r_dihedral_angle_1_deg 4.07
r_angle_other_deg 0.88
r_angle_refined_deg 1.589
r_bond_other_d 0.001
r_bond_refined_d 0.016
r_nbd_other 0.214
r_nbtor_other 0.124
r_xyhbond_nbd_refined 0.168
r_xyhbond_nbd_other 0.02
r_metal_ion_refined 0.098
r_symmetry_vdw_refined 0.454
r_symmetry_vdw_other 0.214
r_symmetry_hbond_refined 0.371
r_mcbond_it 0.75
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.3
Luzzati ESD (R-Free Set) 0.2
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 6072
Nucleic Acid Atoms 0
Heterogen Atoms 12
Solvent Atoms 319

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK, CCP4 (TRUNCATE) Data Reduction (data scaling)
CNS Structure Solution
REFMAC 5 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.0 refinement
CNS model building
SCALEPACK/TRUNCATE data reduction
DENZO data collection