29QD | pdb_000029qd

X-RAY DIFFRACTION

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4CD4

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.6	293	2% tacsimate, 0.1 M Sodium citrate tribasic dihydrate pH 5.6, 16% PEG3350

Crystal Properties
Matthews coefficient	Solvent content
2.81	56.2

Symmetry
Space Group	P 61 2 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 EIGER2 XE 16M		2020-11-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.80	Diamond	I03

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	CC (Half)	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	1.16	73.43	100	0.999	11.6	39		180225		0.5

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	1.16	1.18	100		0.33		6.1

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	1.2	70.469	162967	8303	99.957	0.131	0.1297	0.1297	0.1488	0.1489	12.788

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]
-0.027	-0.014		-0.027		0.088

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.794
r_dihedral_angle_4_deg	16.559
r_dihedral_angle_3_deg	12.081
r_rigid_bond_restr	7.591
r_dihedral_angle_1_deg	6.286
r_scbond_it	3.61
r_scbond_other	3.609
r_scangle_it	3.437
r_scangle_other	3.436
r_lrange_it	3.422

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.794
r_dihedral_angle_4_deg	16.559
r_dihedral_angle_3_deg	12.081
r_rigid_bond_restr	7.591
r_dihedral_angle_1_deg	6.286
r_scbond_it	3.61
r_scbond_other	3.609
r_scangle_it	3.437
r_scangle_other	3.436
r_lrange_it	3.422
r_lrange_other	3.199
r_mcbond_it	2.767
r_mcbond_other	2.632
r_mcangle_other	2.407
r_mcangle_it	2.385
r_angle_refined_deg	1.973
r_angle_other_deg	1.644
r_symmetry_xyhbond_nbd_refined	0.321
r_symmetry_nbd_refined	0.272
r_nbd_refined	0.231
r_nbd_other	0.205
r_nbtor_refined	0.187
r_symmetry_nbd_other	0.184
r_xyhbond_nbd_refined	0.139
r_chiral_restr	0.125
r_metal_ion_refined	0.107
r_symmetry_nbtor_other	0.1
r_bond_refined_d	0.016
r_gen_planes_refined	0.013
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2937
Nucleic Acid Atoms
Solvent Atoms	412
Heterogen Atoms	25

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.