9B02 | pdb_00009b02

nnhA C357A catalytic mutant in tris buffer

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	9AZG

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.2	293	Protein was at 2.5 mg/mL in tris pH 7.0 buffer. The drops were 200 nL plus 200 nL and incubated at 20 C. The reservoir was 21.7% polyacrylic acid 5100, 15 mM MgCl2 and 100 mM HEPES pH 7.2

Crystal Properties
Matthews coefficient	Solvent content
3.29	62.57

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 206.091	α = 90
b = 206.091	β = 90
c = 69.31	γ = 120

Symmetry
Space Group	H 3 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 EIGER R 4M		2016-03-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	AUSTRALIAN SYNCHROTRON BEAMLINE MX1	0.953700	Australian Synchrotron	MX1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	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	40.3	99.8	0.178	0.055	0.996	10.9	11.3		39795

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.97	2.01			0.909	0.289	0.862	2.8

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	1.97	40.3	39787	2086	99.814	0.167	0.1648	0.1857	0.1979	0.2214	18.616

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]
-2.035	-1.017		-2.035		6.601

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	17.942
r_dihedral_angle_3_deg	13.291
r_dihedral_angle_2_deg	9.346
r_dihedral_angle_1_deg	6.923
r_lrange_it	4.96
r_lrange_other	4.959
r_scangle_it	3.578
r_scangle_other	3.578
r_scbond_it	2.304
r_scbond_other	2.303
r_mcangle_other	1.947
r_mcangle_it	1.944
r_angle_refined_deg	1.438
r_mcbond_it	1.307
r_mcbond_other	1.291
r_angle_other_deg	0.505
r_nbd_refined	0.206
r_symmetry_nbd_other	0.183
r_nbtor_refined	0.177
r_xyhbond_nbd_refined	0.16
r_nbd_other	0.159
r_symmetry_nbd_refined	0.151
r_symmetry_xyhbond_nbd_refined	0.141
r_symmetry_nbtor_other	0.075
r_chiral_restr	0.072
r_bond_refined_d	0.008
r_gen_planes_refined	0.008
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2890
Nucleic Acid Atoms
Solvent Atoms	366
Heterogen Atoms	20

Software

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