7QXO | pdb_00007qxo

The structure of T. forsythia NanH

X-RAY DIFFRACTION

---

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	300	7% PEG6000 0.1M HEPES

Crystal Properties
Matthews coefficient	Solvent content
2.43	49.37

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79.868	α = 90
b = 79.868	β = 90
c = 349.449	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		2018-07-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.97795	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	1.9	72.64	100	0.141	0.964	14.4	25.3		90670

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	1.9	1.93	98.29		2.525	0.668	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	1.9	72.64	90497	4483	99.89	0.254	0.2518	0.26	0.2903	0.29	43.051

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]
1.763			1.763		-3.527

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.228
r_dihedral_angle_4_deg	15.757
r_dihedral_angle_3_deg	13.527
r_dihedral_angle_1_deg	7.958
r_lrange_other	4.826
r_lrange_it	4.743
r_scangle_it	1.571
r_scangle_other	1.571
r_angle_refined_deg	1.411
r_mcangle_it	1.405
r_mcangle_other	1.405
r_angle_other_deg	1.177
r_scbond_it	0.988
r_scbond_other	0.988
r_mcbond_it	0.92
r_mcbond_other	0.92
r_nbd_refined	0.18
r_symmetry_nbd_other	0.179
r_nbd_other	0.158
r_nbtor_refined	0.146
r_xyhbond_nbd_refined	0.142
r_symmetry_xyhbond_nbd_refined	0.14
r_symmetry_nbd_refined	0.106
r_ncsr_local_group_1	0.084
r_symmetry_nbtor_other	0.072
r_chiral_restr	0.056
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	8044
Nucleic Acid Atoms
Solvent Atoms	393
Heterogen Atoms	86

Software

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