5OPN | pdb_00005opn

Crystal structure of R39Q cN-II mutant

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5K7Y

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION		293	0.1 M MES/imidazole pH 6.5; 0.02 M of each carboxylic acid; 10% w/v PEG 20 000, 20% v/v PEG MME 550 G1 Morpheus condition

Crystal Properties
Matthews coefficient	Solvent content
3.42	64.06

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 91.469	α = 90
b = 127.115	β = 90
c = 130.218	γ = 90

Symmetry
Space Group	I 2 2 2

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		2016-04-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.1	0.918409	BESSY	14.1

Data Collection

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	1.766	48.45	99.1	0.054	0.063	0.999	16.7	4.6		73833			30.9

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	1.77	1.87	98.9		0.612	0.71	0.719	1.91	3.81

Refinement

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	5K7Y	1.77	48.45	71727	2100	99.13	0.1799	0.1793	0.1887	0.2001	0.2079	RANDOM	30.749

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.257
r_dihedral_angle_4_deg	17.004
r_dihedral_angle_3_deg	12.903
r_dihedral_angle_1_deg	6.026
r_angle_other_deg	3.598
r_angle_refined_deg	1.49
r_chiral_restr	0.095
r_gen_planes_other	0.014
r_bond_refined_d	0.012
r_gen_planes_refined	0.008
r_bond_other_d

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3843
Nucleic Acid Atoms
Solvent Atoms	274
Heterogen Atoms	36

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
MOLREP	phasing
XDS	data reduction
Coot	model building
XDS	data scaling