8A97 | pdb_00008a97

ROOM TEMPERATURE CRYSTAL STRUCTURE OF THE COFACTOR-DEVOID 1-H-3-HYDROXY-4- OXOQUINALDINE 2,4-DIOXYGENASE (HOD) UNDER XENON PRESSURE (30 bar)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2WJ3

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
2	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
2.42	48.22
	48.22

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 44.86	α = 90
b = 169.46	β = 90
c = 169.31	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	2	x-ray	293	PIXEL	DECTRIS PILATUS 6M		2012-07-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I24	0.96860	Diamond	I24

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	2.897	53.583	99.2	0.198	0.061	5.4	4.4		29421			59.9

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	2.897	2.95	95.8		1.12	0.623	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	THROUGHOUT	2WJ3	2.897	53.583	29381	1483	98.806	0.193	0.1918	0.2	0.2203	0.22	62.756

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]
3.482			0.271		-3.753

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.004
r_dihedral_angle_4_deg	15.607
r_dihedral_angle_3_deg	14.172
r_lrange_it	7.364
r_lrange_other	7.364
r_dihedral_angle_1_deg	5.964
r_mcangle_it	4.336
r_mcangle_other	4.336
r_scangle_it	3.91
r_scangle_other	3.91
r_mcbond_it	2.672
r_mcbond_other	2.672
r_scbond_it	2.375
r_scbond_other	2.375
r_angle_other_deg	1.448
r_angle_refined_deg	1.312
r_nbd_other	0.269
r_symmetry_nbd_refined	0.208
r_nbd_refined	0.202
r_symmetry_nbd_other	0.176
r_nbtor_refined	0.174
r_xyhbond_nbd_refined	0.127
r_chiral_restr	0.081
r_symmetry_nbtor_other	0.08
r_symmetry_xyhbond_nbd_refined	0.059
r_ncsr_local_group_4	0.039
r_ncsr_local_group_1	0.035
r_ncsr_local_group_6	0.032
r_ncsr_local_group_5	0.029
r_ncsr_local_group_2	0.027
r_ncsr_local_group_3	0.022
r_ext_dist_refined_d	0.01
r_bond_refined_d	0.008
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	8966
Nucleic Acid Atoms
Solvent Atoms	49
Heterogen Atoms	54

Software

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