7OJM | pdb_00007ojm

CRYSTAL STRUCTURE OF THE COFACTOR-DEVOID 1-H-3-HYDROXY-4- OXOQUINALDINE 2,4-DIOXYGENASE (HOD) CATALYTICALLY INACTIVE H251A VARIANT COMPLEXED WITH 2-METHYL-QUINOLIN-4(1H)-ONE UNDER NORMOXIC CONDITIONS

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4CFS

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7	293	PROTEIN AT 150 MG/ML IN STORAGE BUFFER 1.65M NA/K TARTRATE, 0.1M HEPES PH 7.0

Crystal Properties
Matthews coefficient	Solvent content
2.38	48.22

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 119.19	α = 90
b = 119.19	β = 90
c = 44.44	γ = 90

Symmetry
Space Group	P 41

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 PILATUS 6M		2015-01-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.91741	Diamond	I04-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	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	2	44.44	99.3	0.108	0.05	10.5	6.4		42360			27.6

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2	2.05			0.737	0.407	1.8

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	4CFS	2.001	42.14	42343	2116	99.243	0.206	0.2041	0.21	0.2367	0.24	32.536

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]
8.048			8.048		-16.096

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.832
r_dihedral_angle_4_deg	19.131
r_dihedral_angle_3_deg	15.157
r_dihedral_angle_1_deg	6.766
r_lrange_it	5.225
r_lrange_other	5.128
r_scangle_it	3.131
r_scangle_other	3.131
r_mcangle_it	3.12
r_mcangle_other	3.12
r_mcbond_it	2.133
r_mcbond_other	2.133
r_scbond_it	2.097
r_scbond_other	2.097
r_angle_refined_deg	1.335
r_angle_other_deg	1.183
r_nbd_other	0.296
r_symmetry_nbd_refined	0.244
r_metal_ion_refined	0.242
r_xyhbond_nbd_refined	0.217
r_nbd_refined	0.206
r_symmetry_nbd_other	0.193
r_symmetry_xyhbond_nbd_refined	0.17
r_nbtor_refined	0.161
r_symmetry_xyhbond_nbd_other	0.126
r_symmetry_nbtor_other	0.078
r_chiral_restr	0.064
r_ncsr_local_group_1	0.028
r_gen_planes_refined	0.006
r_bond_refined_d	0.005
r_bond_other_d	0.003
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4444
Nucleic Acid Atoms
Solvent Atoms	244
Heterogen Atoms	86

Software

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