9RY3 | pdb_00009ry3

X-RAY DIFFRACTION

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

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		291	55 mM KCl, 85 mM MnCl2, 20 mM K-Cacodylate (pH 6.0)

Crystal Properties
Matthews coefficient	Solvent content
2.7	54.47

Symmetry
Space Group	P 21 21 21

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	90	PIXEL	DECTRIS PILATUS 2M		2012-07-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06DA	1.5	SLS	X06DA

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	2.75	48.89	99.6	1	20.1	6		56299

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	2.75	2.9			0.447

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	2.75	48.89	56236	1182	99.517	0.221	0.2202	0.2209	0.2688	0.2111	115.258

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]
0.324			-5.092		4.768

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	16.339
r_lrange_it	16.297
r_lrange_other	16.297
r_dihedral_angle_6_deg	15.583
r_scangle_it	12.516
r_scangle_other	12.516
r_mcangle_it	8.79
r_mcangle_other	8.789
r_scbond_it	8.078
r_scbond_other	8.078

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	16.339
r_lrange_it	16.297
r_lrange_other	16.297
r_dihedral_angle_6_deg	15.583
r_scangle_it	12.516
r_scangle_other	12.516
r_mcangle_it	8.79
r_mcangle_other	8.789
r_scbond_it	8.078
r_scbond_other	8.078
r_mcbond_it	6.036
r_mcbond_other	6.029
r_dihedral_angle_1_deg	5.532
r_dihedral_angle_2_deg	5.437
r_angle_refined_deg	1.384
r_dihedral_angle_other_2_deg	0.82
r_angle_other_deg	0.44
r_nbtor_refined	0.214
r_symmetry_nbd_other	0.211
r_nbd_refined	0.205
r_symmetry_xyhbond_nbd_refined	0.198
r_symmetry_nbd_refined	0.168
r_xyhbond_nbd_refined	0.156
r_nbd_other	0.155
r_symmetry_xyhbond_nbd_other	0.108
r_symmetry_nbtor_other	0.076
r_chiral_restr	0.056
r_bond_refined_d	0.004
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6086
Nucleic Acid Atoms	5939
Solvent Atoms
Heterogen Atoms	50

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.