5LBR | pdb_00005lbr

Wild-type PAS-GAF fragment from Deinococcus radiodurans Bphp collected at SACLA

X-RAY DIFFRACTION

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Serial Crystallography (SX)

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4Q0H

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.95	298	Sodium Acetate, Peg400, 2-methyl-2,4-pentanediol

Crystal Properties
Matthews coefficient	Solvent content
2.57	52.05

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 96.22	α = 90
b = 55.49	β = 92.84
c = 71.63	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	298	CCD	MPCCD		2015-02-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	FREE ELECTRON LASER	SACLA BEAMLINE BL3	0.987	SACLA	BL3

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	CC (Half)	R Split (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	2.2	71.54	100	0.976	0.119	5.62	81.2		18818

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Split (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.2	2.28	100		0.677	0.68	24.1

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	4Q0H	2.2	71.54	18389	956	100	0.18084	0.1821	0.19	0.2033	0.22	RANDOM	50.258

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]
0.36		-0.76	0.44		-0.72

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.627
r_dihedral_angle_3_deg	13.566
r_dihedral_angle_4_deg	12.759
r_long_range_B_refined	6.758
r_long_range_B_other	6.757
r_dihedral_angle_1_deg	6.216
r_scangle_other	4.406
r_mcangle_it	3.599
r_mcangle_other	3.599
r_scbond_it	2.593
r_scbond_other	2.592
r_mcbond_it	2.196
r_mcbond_other	2.191
r_angle_refined_deg	1.287
r_angle_other_deg	0.913
r_chiral_restr	0.072
r_bond_refined_d	0.008
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2328
Nucleic Acid Atoms
Solvent Atoms	117
Heterogen Atoms	47

Software

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