5VRD | pdb_00005vrd

Crystal structure for Methylobacterium extorquens PqqCD (natural fusion)

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		292	500 microL well volumes. Protein solution: 8.0 mg/mL protein, 50 mM Tris, pH 7.9, 100 mM sodium chloride, and 1 mM TCEP. Well solution: 100 mM HEPES, pH 6.7, 19% w/v PEG-4000, 10% isopropanol. Water used in the well solutions contained 0.55 mM sodium azide. Hanging drops were 1 microL protein solution and 1 microL well solution

Crystal Properties
Matthews coefficient	Solvent content
2.9	57.52

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 103.936	α = 90
b = 103.936	β = 90
c = 243.485	γ = 90

Symmetry
Space Group	P 41 21 2

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 PILATUS3 6M		2015-10-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-D	1.0332	APS	23-ID-D

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	2.85	243.49	98.5	0.062	0.032	17	4.5		31557

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	1otv	2.85	243.49	29899	1593	98.38	0.2569	0.25314	0.26	0.32707	0.33	RANDOM

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]
1.09			1.09		-2.17

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.886
r_dihedral_angle_3_deg	21.46
r_dihedral_angle_4_deg	18.939
r_long_range_B_refined	8.509
r_long_range_B_other	8.503
r_dihedral_angle_1_deg	8.119
r_mcangle_other	5.641
r_mcangle_it	5.64
r_scangle_other	5.496
r_mcbond_it	3.615
r_mcbond_other	3.613
r_scbond_it	3.444
r_scbond_other	3.444
r_angle_refined_deg	2.088
r_angle_other_deg	1.241
r_chiral_restr	0.119
r_bond_refined_d	0.018
r_gen_planes_refined	0.009
r_bond_other_d	0.002
r_gen_planes_other	0.002
r_scangle_it

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6570
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

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