7QYP | pdb_00007qyp

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
2.43	49.34

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79.895	α = 90
b = 79.895	β = 90
c = 349.328	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 PILATUS3 6M		2017-12-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.97951	Diamond	I04

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.659	79.89	100	0.168	0.992	6.9	12.1		135097

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.66	1.69	99.21		0.851	0.435	0.9

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	1.659	78.005	133326	6556	98.77	0.224	0.2218	0.22	0.2727	0.27	29.929

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]
0.764			0.764		-1.529

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.129
r_dihedral_angle_4_deg	14.714
r_dihedral_angle_3_deg	12.289
r_lrange_other	11.131
r_lrange_it	11.082
r_scangle_it	10.725
r_scangle_other	10.725
r_scbond_it	10.58
r_scbond_other	10.579
r_dihedral_angle_1_deg	8.163
r_mcbond_it	7.106
r_mcbond_other	7.106
r_mcangle_it	6.747
r_mcangle_other	6.747
r_angle_refined_deg	1.681
r_angle_other_deg	1.357
r_nbd_refined	0.198
r_symmetry_nbd_other	0.188
r_symmetry_nbd_refined	0.178
r_nbd_other	0.176
r_nbtor_refined	0.155
r_xyhbond_nbd_refined	0.155
r_symmetry_xyhbond_nbd_refined	0.126
r_symmetry_xyhbond_nbd_other	0.105
r_ncsr_local_group_1	0.089
r_chiral_restr	0.079
r_symmetry_nbtor_other	0.078
r_bond_refined_d	0.012
r_gen_planes_refined	0.009
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8046
Nucleic Acid Atoms
Solvent Atoms	704
Heterogen Atoms	40

Software

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