X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 4.5
Temperature 293.0
Details Ammonium sulfate, Citrate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 37.01 α = 90
b = 60.97 β = 90
c = 67.38 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD RIGAKU -- --
Diffraction Radiation
Monochromator Protocol
180 degree SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU MICROMAX-007 HF 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 50 98.1 0.073 -- -- 6.9 10308 10112 2.0 2.0 --
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)
2.0 2.05 93.5 0.37 -- 5.6 6.7 --

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 2.0 45.22 -- -- -- 10112 511 98.03 -- 0.18807 0.18501 0.25147 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 1.998 2.049 -- 37 710 0.223 0.38 -- 93.96
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 23.293
Anisotropic B[1][1] 0.24
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -1.5
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 1.25
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 3.858
r_scbond_it 2.379
r_mcangle_it 1.324
r_mcbond_it 0.934
r_symmetry_hbond_refined 0.175
r_bond_refined_d 0.014
r_angle_refined_deg 1.302
r_dihedral_angle_1_deg 5.559
r_dihedral_angle_2_deg 38.752
r_dihedral_angle_3_deg 15.113
r_dihedral_angle_4_deg 21.04
r_chiral_restr 0.083
r_gen_planes_refined 0.005
r_nbd_refined 0.205
r_nbtor_refined 0.294
r_xyhbond_nbd_refined 0.139
r_symmetry_vdw_refined 0.152
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1154
Nucleic Acid Atoms 0
Heterogen Atoms 25
Solvent Atoms 102

Software

Computing
Computing Package Purpose
HKL-2000 Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
PHASES Structure Solution
REFMAC 5.2.0019 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.2.0019 refinement
PHASES model building
HKL-2000 data collection