3VEG | pdb_00003veg

Rhodococcus jostii RHA1 DypB R244L variant in complex with heme

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3QNR	PDB ENTRY 3QNR

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.5	293	0.1 M sodium acetate trihydrate, 3 M sodium chloride, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.62	66.02

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 133.224	α = 90
b = 133.224	β = 90
c = 158.922	γ = 120

Symmetry
Space Group	P 32 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	RAYONIX MX300HE	Collimating Mirror with two stripes (Si, Rh/Pt), Toroidal Focusing Mirror (Rh/Pt)	2010-12-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CLSI BEAMLINE 08B1-1	0.97952	CLSI	08B1-1

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	2.35	115.375	99.9	0.096	10.8	6		67790

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	2.35	2.43	100		0.516		6	6698

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 3QNR	2.35	53	67577	3429	99.36	0.1876	0.1858	0.1825	0.2218	0.2184	RANDOM	39.1026

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]
-1.19	-0.6		-1.19		1.79

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.422
r_dihedral_angle_4_deg	19.605
r_dihedral_angle_3_deg	15.204
r_dihedral_angle_1_deg	5.654
r_scangle_it	3.087
r_scbond_it	1.885
r_mcangle_it	1.504
r_angle_refined_deg	1.33
r_mcbond_it	0.805
r_chiral_restr	0.088
r_bond_refined_d	0.013
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7018
Nucleic Acid Atoms
Solvent Atoms	407
Heterogen Atoms	132

Software

Software
Software Name	Purpose
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MxDC	data collection
HKL-2000	data reduction
HKL-2000	data scaling
REFMAC	phasing