8PQN | pdb_00008pqn

NQO1 bound to RBS-10

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1D4A

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	9.2	293	300mM TRIS 9.2 2.8M Ammonium Sulfate

Crystal Properties
Matthews coefficient	Solvent content
2.77	55.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 70.748	α = 90
b = 178.369	β = 90
c = 210.479	γ = 90

Symmetry
Space Group	C 2 2 21

Diffraction

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	Kirkpatrick-Baez	2023-04-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALBA BEAMLINE XALOC	0.97918	ALBA	XALOC

Data Collection

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	3.8	89.18	100	0.079	11.4	6.1		13579			121.5

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.8	4.01	100		0.495	4.1	6.2

Refinement

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	3.8	68.132	13543	687	99.904	0.266	0.261	0.27	0.3616	0.36	209.703

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]
31.519			-11.45		-20.069

RMS Deviations
Key	Refinement Restraint Deviation
r_lrange_it	24.007
r_lrange_other	24.006
r_mcangle_it	17.181
r_mcangle_other	17.18
r_scangle_it	14.056
r_scangle_other	14.055
r_dihedral_angle_3_deg	14.012
r_dihedral_angle_6_deg	11.011
r_mcbond_it	10.391
r_mcbond_other	10.39
r_scbond_it	8.074
r_scbond_other	8.063
r_dihedral_angle_1_deg	7.5
r_dihedral_angle_2_deg	2.302
r_angle_refined_deg	0.894
r_angle_other_deg	0.313
r_symmetry_nbd_refined	0.256
r_nbd_other	0.227
r_symmetry_nbd_other	0.191
r_nbd_refined	0.18
r_nbtor_refined	0.179
r_xyhbond_nbd_refined	0.164
r_symmetry_xyhbond_nbd_other	0.144
r_symmetry_nbtor_other	0.075
r_chiral_restr	0.041
r_chiral_restr_other	0.01
r_bond_refined_d	0.004
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8696
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	160

Software

Software
Software Name	Purpose
MxCuBE	data collection
iMOSFLM	data reduction
pointless	data scaling
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
Coot	model building