Experiment: 4NO8

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.8	293	20 mM MgAc2, 100 mM MES, 13% MPD, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.69	66.65

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 134.15	α = 90
b = 300.35	β = 112.48
c = 144.83	γ = 90

Symmetry
Space Group	P 1 21 1

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	PSI PILATUS 6M		2013-07-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	1.0	SLS	X06SA

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	2.7	40	97.2	0.06	13.25	2.7	289277	281177	2	2

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	2.7	2.8	98.2		0.498	1.83

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	1RYP	2.7	15	281177	267118	14059	97.34	0.198	0.19379	0.19258	0.2	0.21689	0.23	RANDOM	58.118

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]
4.38		-3.89	-6.86		3.05

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	45.882
r_dihedral_angle_2_deg	36.362
r_dihedral_angle_3_deg	17.62
r_dihedral_angle_4_deg	16.709
r_sphericity_bonded	9.074
r_dihedral_angle_1_deg	6
r_angle_refined_deg	0.993
r_rigid_bond_restr	0.924
r_angle_other_deg	0.727
r_chiral_restr	0.057

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	45.882
r_dihedral_angle_2_deg	36.362
r_dihedral_angle_3_deg	17.62
r_dihedral_angle_4_deg	16.709
r_sphericity_bonded	9.074
r_dihedral_angle_1_deg	6
r_angle_refined_deg	0.993
r_rigid_bond_restr	0.924
r_angle_other_deg	0.727
r_chiral_restr	0.057
r_bond_refined_d	0.005
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	49296
Nucleic Acid Atoms
Solvent Atoms	488
Heterogen Atoms	94

Software

Software
Software Name	Purpose
XDS	data scaling
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
REFMAC	phasing

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.