6Y01

The structure of the molybdenum cofactor binding protein from the phototrophic bacterium Rippkaea orientalis

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	292	15% (v/v) Pentaerythritol ethoxylate; 0.2 M potassium acetate; 3% (v/v) Jeffamine T-403; 0.1 M MES pH 6.0

Crystal Properties
Matthews coefficient	Solvent content
2.12	41.88

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 68.577	α = 90
b = 72.044	β = 113.333
c = 70.264	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	PIXEL	DECTRIS PILATUS 2M-F	TOROIDAL FOCUSING MIRRORS	2015-05-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06DA	1.00003	SLS	X06DA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	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	1.23	64.52	100	0.05279	0.05719	0.02177	1	16.35	6.7		181674		-3	15.66

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.23	1.274	100		3.026	3.299	1.297	0.193	0.55	6.3

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2IZ6	1.23	64.518	181736	8868	99.999	0.143	0.1418	0.1629	RANDOM	27.869

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]
0.509		3.035	-3.184		0.042

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.031
r_dihedral_angle_4_deg	17.84
r_dihedral_angle_3_deg	11.621
r_dihedral_angle_1_deg	5.334
r_rigid_bond_restr	5.013
r_lrange_it	4.121
r_lrange_other	4.023
r_scangle_it	3.917
r_scangle_other	3.917
r_scbond_it	3.335
r_scbond_other	3.334
r_mcangle_other	2.705
r_mcangle_it	2.704
r_mcbond_it	2.266
r_mcbond_other	2.264
r_angle_refined_deg	1.845
r_angle_other_deg	1.691
r_nbd_other	0.282
r_nbd_refined	0.234
r_symmetry_nbd_refined	0.224
r_symmetry_nbd_other	0.191
r_nbtor_refined	0.163
r_xyhbond_nbd_refined	0.141
r_chiral_restr	0.108
r_symmetry_xyhbond_nbd_refined	0.108
r_ncsr_local_group_6	0.108
r_ncsr_local_group_5	0.107
r_ncsr_local_group_3	0.099
r_ncsr_local_group_2	0.088
r_symmetry_nbtor_other	0.082
r_ncsr_local_group_1	0.081
r_ncsr_local_group_4	0.079
r_bond_refined_d	0.019
r_gen_planes_refined	0.01
r_bond_other_d	0.007
r_gen_planes_other	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4774
Nucleic Acid Atoms
Solvent Atoms	393
Heterogen Atoms	20

Software

Software
Software Name	Purpose
XDS	data processing
Aimless	data scaling
PHASER	phasing
SHELXE	model building
Coot	model building
REFMAC	refinement