3G14 | pdb_00003g14

Crystal structure of nitroreductase family protein (YP_877874.1) from Clostridium novyi NT at 1.75 A resolution

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.29	277	NANODROP, 0.160M Ammonium sulfate, 22.3% PEG 4000, 20.0% Glycerol, 0.1M Sodium acetate pH 4.29, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
1.99	38.14

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.35	α = 90
b = 44.95	β = 93.72
c = 66.96	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	MARMOSAIC 325 mm CCD	Flat mirror (vertical focusing)	2008-11-15	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.91837, 0.97876, 0.97826	SSRL	BL11-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.75	28.194	97.2	0.056				34941		-3	20.426

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.75	1.81	90.2		0.499	1.4

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	1.75	28.194	34929	1754	99.35	0.176	0.173	0.18	0.219	0.22	RANDOM	21.923

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]
-0.82		-0.26	0.43		0.36

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.611
r_dihedral_angle_3_deg	13.664
r_dihedral_angle_4_deg	9.369
r_scangle_it	6.891
r_dihedral_angle_1_deg	5.42
r_scbond_it	5.128
r_mcangle_it	2.682
r_mcbond_it	2.027
r_angle_refined_deg	1.462
r_angle_other_deg	0.937
r_mcbond_other	0.536
r_symmetry_vdw_other	0.231
r_symmetry_vdw_refined	0.219
r_nbd_refined	0.211
r_nbd_other	0.182
r_nbtor_refined	0.172
r_xyhbond_nbd_refined	0.146
r_symmetry_hbond_refined	0.124
r_chiral_restr	0.087
r_nbtor_other	0.085
r_bond_refined_d	0.016
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	2775
Nucleic Acid Atoms
Solvent Atoms	275
Heterogen Atoms	32

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
MAR345	data collection
XDS	data reduction
SHELXD	phasing
autoSHARP	phasing