Experiment: 9YD2

X-RAY DIFFRACTION

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

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		290	46% (v/v) saturated ammonium sulfate, 10 mM manganese sulfate (MnSO4), 100 mM 2-(N-morpholino)ethanesulfonic acid (MES), 5% 2-methyl-1,3-propanediol (MPD), 1 mM 2',3'-dideoxyguanosine triphosphate, 5 mM 2'-deoxyadenosine triphosphate

Crystal Properties
Matthews coefficient	Solvent content
3.14	60.59

Symmetry
Space Group	P 31 2 1

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	MARMOSAIC 225 mm CCD		2015-03-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-BM	1.000	APS	22-BM

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim I (All)	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	2.249	79.8	99.3	0.063	0.999	21.64	6.9		44763

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.249	2.31	92.4		1	0.616	1.42	4.6

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	2.249	79.796	44763	2372	99.229	0.228	0.2247	0.231	0.2853	0.286	57.896

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]
0.001	0.001		0.001		-0.004

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	16.61
r_dihedral_angle_6_deg	14.523
r_lrange_other	13.615
r_lrange_it	13.608
r_scangle_it	10.642
r_scangle_other	10.575
r_dihedral_angle_2_deg	9.683
r_mcangle_it	8.319
r_mcangle_other	8.319
r_scbond_it	7.122

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	16.61
r_dihedral_angle_6_deg	14.523
r_lrange_other	13.615
r_lrange_it	13.608
r_scangle_it	10.642
r_scangle_other	10.575
r_dihedral_angle_2_deg	9.683
r_mcangle_it	8.319
r_mcangle_other	8.319
r_scbond_it	7.122
r_scbond_other	7.077
r_dihedral_angle_1_deg	7.054
r_mcbond_it	5.889
r_mcbond_other	5.888
r_angle_refined_deg	1.948
r_angle_other_deg	0.642
r_dihedral_angle_other_2_deg	0.609
r_nbd_refined	0.241
r_symmetry_nbd_other	0.2
r_symmetry_nbd_refined	0.198
r_nbtor_refined	0.19
r_xyhbond_nbd_refined	0.18
r_symmetry_xyhbond_nbd_refined	0.158
r_nbd_other	0.145
r_symmetry_xyhbond_nbd_other	0.107
r_chiral_restr	0.09
r_symmetry_nbtor_other	0.083
r_xyhbond_nbd_other	0.036
r_bond_refined_d	0.009
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4651
Nucleic Acid Atoms	505
Solvent Atoms	98
Heterogen Atoms	46

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.

9YD2 | pdb_00009yd2