7QZ3 | pdb_00007qz3

The structure of T. forsythia NanH

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	290	7% PEG6000 0.1M HEPES

Crystal Properties
Matthews coefficient	Solvent content
2.42	49.17

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79.74	α = 90
b = 79.74	β = 90
c = 349.5	γ = 90

Symmetry
Space Group	P 41 21 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		2015-12-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9763	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	1.97	77.863	99.4	1	21.8	3.81		80616

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.97	2.01			0.472	1.3

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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	4bbw	1.97	77.863	80615	3899	99.314	0.232	0.2304	0.23	0.2662	0.27	43.851

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]
2.005			2.005		-4.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.344
r_dihedral_angle_4_deg	13.978
r_dihedral_angle_3_deg	12.743
r_dihedral_angle_1_deg	8.111
r_lrange_it	4.071
r_lrange_other	4.043
r_scangle_it	1.879
r_scangle_other	1.879
r_mcangle_it	1.746
r_mcangle_other	1.746
r_angle_refined_deg	1.35
r_scbond_it	1.219
r_scbond_other	1.215
r_mcbond_it	1.19
r_mcbond_other	1.19
r_angle_other_deg	1.17
r_symmetry_xyhbond_nbd_refined	0.232
r_nbd_refined	0.181
r_symmetry_nbd_other	0.174
r_nbd_other	0.162
r_xyhbond_nbd_refined	0.151
r_nbtor_refined	0.147
r_ncsr_local_group_1	0.077
r_symmetry_nbd_refined	0.074
r_symmetry_nbtor_other	0.07
r_chiral_restr	0.054
r_bond_refined_d	0.005
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8046
Nucleic Acid Atoms
Solvent Atoms	425
Heterogen Atoms	30

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
Aimless	data scaling
PHASER	phasing