9B01 | pdb_00009b01

Catalytic mutant C357A nnhA in CHES buffer

X-RAY DIFFRACTION

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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 CHES buffer at pH 9.0 and was set up in 200 nL plus 200 nL drops at 20 C. The reservoir was 21.2% polyacrylic acid 5100, 30 mM MgCl2 and 100 mM HEPES at pH 7.2

Crystal Properties
Matthews coefficient	Solvent content
3.24	61.98

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 206.124	α = 90
b = 206.124	β = 90
c = 68.215	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	1.99	48	99.9	0.231	0.072	0.993	9.7	11.3		37832

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	1.99	2.04	98.3		1.011	0.322	0.83	2.7	10.6

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	1.99	48	37832	1967	99.834	0.147	0.146	0.1527	0.1738	0.1817	14.262

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]
-1.159	-0.58		-1.159		3.76

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.927
r_dihedral_angle_3_deg	11.602
r_dihedral_angle_2_deg	10.198
r_dihedral_angle_1_deg	6.916
r_lrange_it	4.799
r_lrange_other	4.799
r_scangle_it	3.384
r_scangle_other	3.384
r_scbond_other	2.19
r_scbond_it	2.189
r_angle_refined_deg	1.598
r_mcangle_other	1.591
r_mcangle_it	1.589
r_mcbond_it	1.04
r_mcbond_other	1.04
r_angle_other_deg	0.568
r_nbd_refined	0.215
r_symmetry_xyhbond_nbd_refined	0.193
r_symmetry_nbd_other	0.188
r_nbtor_refined	0.18
r_xyhbond_nbd_refined	0.164
r_nbd_other	0.164
r_symmetry_nbd_refined	0.143
r_chiral_restr	0.081
r_symmetry_nbtor_other	0.079
r_bond_refined_d	0.008
r_gen_planes_refined	0.007
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	414
Heterogen Atoms	14

Software

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