9RYG | pdb_00009ryg

Bifunctional Non-haem Iron Oxygenase NovR Involved in Novobiocin Biosynthesis with product bound

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1E4C

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	291	NULL

Crystal Properties
Matthews coefficient	Solvent content
2.45	50

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 86.508	α = 90
b = 138.968	β = 101.444
c = 100.615	γ = 90

Symmetry
Space Group	C 1 2 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	ADSC QUANTUM 210		2006-02-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-1	0.934	ESRF	ID14-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim 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	1.79	56.89	97.5	0.079	0.086	13.5	4.9		106383			22

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.79	1.89	84.7		0.509	0.627	2.1	2.6

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	1.791	49.356	106276	5347	97.406	0.162	0.1608	0.1609	0.1883	0.1883	32.17

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]
-0.55		1.331	-0.397		0.378

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.484
r_dihedral_angle_3_deg	13.092
r_dihedral_angle_2_deg	8.488
r_lrange_it	7.931
r_dihedral_angle_1_deg	6.08
r_scangle_it	4.425
r_scbond_it	2.909
r_mcangle_it	2.626
r_angle_refined_deg	1.826
r_mcbond_it	1.708
r_nbtor_refined	0.311
r_nbd_refined	0.199
r_symmetry_xyhbond_nbd_refined	0.182
r_xyhbond_nbd_refined	0.172
r_symmetry_nbd_refined	0.153
r_chiral_restr	0.111
r_ncsr_local_group_3	0.082
r_ncsr_local_group_4	0.08
r_ncsr_local_group_6	0.079
r_ncsr_local_group_1	0.075
r_ncsr_local_group_2	0.074
r_ncsr_local_group_5	0.069
r_bond_refined_d	0.01
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8113
Nucleic Acid Atoms
Solvent Atoms	883
Heterogen Atoms	154

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
AMoRE	phasing