5FMM | pdb_00005fmm

crystal structure of the mid, cap-binding, mid-link and 627 domains from avian influenza a virus polymerase PB2 subunit bound to M7GTP

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4WSB	PDB ENTRIES 4WSB, 4CB4, 3KC6
experimental model	PDB	4CB4	PDB ENTRIES 4WSB, 4CB4, 3KC6
experimental model	PDB	3KC6	PDB ENTRIES 4WSB, 4CB4, 3KC6

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		5		0.1 M TRI-SODIUM CITRATE PH 5 10 % POLYETHYLENE GLYCOL MONOMETHYL ETHER 5000

Crystal Properties
Matthews coefficient	Solvent content
3.1	60.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 97.27	α = 90
b = 97.27	β = 90
c = 126.22	γ = 120

Symmetry
Space Group	P 32 2 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	DECTRIS PILATUS 2M		2015-01-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29		ESRF	ID29

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	2.4	50	100	0.15	12.2	10.5		26542

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	2.4	2.48	100		1.31	2.04	10.5

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 (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	PDB ENTRIES 4WSB, 4CB4, 3KC6	2.4	84.24	26430	1145	99.96	0.21329	0.21242	0.22	0.23368	0.24	RANDOM	75.89

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]
0.77	0.39		0.77		-2.51

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.552
r_dihedral_angle_4_deg	13.627
r_dihedral_angle_3_deg	12.914
r_dihedral_angle_1_deg	5.139
r_mcangle_it	3.93
r_mcbond_it	2.257
r_mcbond_other	2.256
r_scbond_it	2.215
r_angle_refined_deg	1.23
r_angle_other_deg	0.851
r_chiral_restr	0.061
r_bond_refined_d	0.007
r_gen_planes_refined	0.004
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_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3352
Nucleic Acid Atoms
Solvent Atoms	125
Heterogen Atoms	46

Software

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