7KD4 | pdb_00007kd4

Structure of the C-terminal domain of the Menangle virus phosphoprotein (residues 329 -388), fused to MBP. Space group P21.

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4KYC

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	291.15	1.65 M Ammonium sulphate, 0.2M Malic acid/KOH pH 5.5, Crystals were transferred into the following cryo-protective solution before vitrification: 1.65 M Ammonium sulphate, 0.2M Malic acid/KOH pH 5.5, 5mM Maltose, 1 M Lithium sulfate

Crystal Properties
Matthews coefficient	Solvent content
2.38	48.25

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.561	α = 90
b = 70.074	β = 96.472
c = 111.739	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	110	CCD	ADSC QUANTUM 210		2016-10-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	AUSTRALIAN SYNCHROTRON BEAMLINE MX1	0.9537	Australian Synchrotron	MX1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	1.31	59.33	70.7	0.051	0.061	0.032	10.9	3.2		149703			12.824

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.31	1.33	2.9		0.607	0.857	0.605	0.783		1.5

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	4kyc	1.312	59.329	149527	7389	71.002	0.152	0.1498	0.15	0.1957	0.2	Random Selection	13.824

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]
-0.787		-0.763	-0.354		1.281

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.487
r_sphericity_free	24.246
r_dihedral_angle_4_deg	16.625
r_dihedral_angle_3_deg	12.58
r_sphericity_bonded	10.995
r_dihedral_angle_1_deg	5.47
r_lrange_it	3.196
r_scangle_it	2.277
r_scbond_it	1.863
r_rigid_bond_restr	1.737
r_mcangle_it	1.488
r_angle_refined_deg	1.454
r_mcbond_it	1.139
r_nbtor_refined	0.311
r_symmetry_nbd_refined	0.237
r_nbd_refined	0.199
r_symmetry_xyhbond_nbd_refined	0.182
r_xyhbond_nbd_refined	0.14
r_chiral_restr	0.098
r_bond_refined_d	0.009
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6636
Nucleic Acid Atoms
Solvent Atoms	1321
Heterogen Atoms	126

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
PHASER	phasing
Coot	model building