Experiment: 9IBT

X-RAY DIFFRACTION

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3TTQ

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		285	0.1M SPG Buffer pH 7, 20% PEG 1500

Crystal Properties
Matthews coefficient	Solvent content
4.03	69.45

Symmetry
Space Group	H 3 2

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS 6M		2018-12-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE MASSIF-3	0.9677	ESRF	MASSIF-3

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	3.3	50	100	0.189	3.7	8.6		63973

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.3	3.48			0.82	1

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	3.3	48.412	63971	3137	99.947	0.202	0.2007	0.2034	0.2252	0.2257	66.677

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
0.755	0.378		0.755		-2.45

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	12.951
r_dihedral_angle_6_deg	12.41
r_dihedral_angle_1_deg	6.622
r_lrange_it	5.554
r_lrange_other	5.554
r_dihedral_angle_2_deg	4.144
r_mcangle_it	2.481
r_mcangle_other	2.481
r_scangle_it	2.123
r_scangle_other	2.123

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	12.951
r_dihedral_angle_6_deg	12.41
r_dihedral_angle_1_deg	6.622
r_lrange_it	5.554
r_lrange_other	5.554
r_dihedral_angle_2_deg	4.144
r_mcangle_it	2.481
r_mcangle_other	2.481
r_scangle_it	2.123
r_scangle_other	2.123
r_mcbond_it	1.378
r_mcbond_other	1.378
r_scbond_it	1.145
r_scbond_other	1.145
r_angle_refined_deg	0.9
r_angle_other_deg	0.393
r_symmetry_nbd_other	0.221
r_nbd_refined	0.206
r_nbd_other	0.18
r_nbtor_refined	0.175
r_xyhbond_nbd_refined	0.137
r_symmetry_xyhbond_nbd_other	0.133
r_symmetry_nbd_refined	0.132
r_ncsr_local_group_1	0.104
r_symmetry_nbtor_other	0.075
r_symmetry_xyhbond_nbd_refined	0.074
r_chiral_restr	0.045
r_gen_planes_refined	0.003
r_bond_refined_d	0.002
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	18147
Nucleic Acid Atoms
Solvent Atoms	11
Heterogen Atoms	484

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.

9IBT | pdb_00009ibt