6RQ7 | pdb_00006rq7

X-RAY DIFFRACTION

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5OKL	5OKL_B

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	293	Stock: 5 mg/ml AFM in 20mM HEPES pH 7.5, 150mM NaCl, incubated with 10mM Gd-DO3A Drop: 200 nL AFM stock + 200 nL of precipitate in hanging drop vapor diffusion (EMBL HTX) Precipitant: 23 to 28% PEG4k, 0.2M NH4SO4, 0.1 M CH3COONH4, pH 5.5

Crystal Properties
Matthews coefficient	Solvent content
2.05	40

Symmetry
Space Group	P 21 21 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 PILATUS3 2M	BE CRL	2018-05-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE MASSIF-1	0.96598	ESRF	MASSIF-1

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.69	75.24	85.2	0.18	0.2	0.99	5.6	4.7		9591			59.1

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.7	3.02	62		0.54	0.68	0.8	1.7	2.1

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	5OKL_B	2.69	75.24	9041	482	59.59	0.26629	0.26257	0.27	0.33544	0.34	RANDOM	56.545

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]
-0.61			-0.67		1.28

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.84
r_dihedral_angle_3_deg	18.934
r_dihedral_angle_4_deg	11.986
r_long_range_B_refined	10.57
r_long_range_B_other	10.568
r_scangle_other	7.348
r_mcangle_it	6.902
r_mcangle_other	6.902
r_dihedral_angle_1_deg	5.599
r_scbond_it	4.315

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.84
r_dihedral_angle_3_deg	18.934
r_dihedral_angle_4_deg	11.986
r_long_range_B_refined	10.57
r_long_range_B_other	10.568
r_scangle_other	7.348
r_mcangle_it	6.902
r_mcangle_other	6.902
r_dihedral_angle_1_deg	5.599
r_scbond_it	4.315
r_scbond_other	4.314
r_mcbond_it	4.21
r_mcbond_other	4.209
r_angle_refined_deg	1.191
r_angle_other_deg	1.029
r_chiral_restr	0.04
r_gen_planes_refined	0.003
r_bond_refined_d	0.002
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3866
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	143