6M2Y | pdb_00006m2y

Crystal structure of a formolase, BFD variant M6 from Pseudomonas putida

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6A50

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	295	0.1 M acetate pH 4.5, 0.2 M NaCl,40% (v/v) PEG-300

Crystal Properties
Matthews coefficient	Solvent content
2.85	56.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 103.515	α = 90
b = 106.674	β = 90
c = 116.548	γ = 90

Symmetry
Space Group	I 2 2 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 S 6M		2019-12-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL18U1	1.0	SSRF	BL18U1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	2.06	25	100	0.245	0.255	0.072	3.5	12.4		39009

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	2.1	2.18	100		1.025	1.082	0.342	0.849		9.4

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	6A50	2.1	24.6	36101	1848	99.91	0.1558	0.154	0.155	0.1891	0.1887	RANDOM	16.587

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]
-1.51			1.47		0.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.322
r_dihedral_angle_4_deg	15.5
r_dihedral_angle_3_deg	14.35
r_dihedral_angle_1_deg	6.41
r_angle_refined_deg	2.254
r_angle_other_deg	1.219
r_chiral_restr	0.086
r_bond_refined_d	0.017
r_gen_planes_refined	0.007
r_bond_other_d
r_gen_planes_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3954
Nucleic Acid Atoms
Solvent Atoms	446
Heterogen Atoms	27

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data scaling
PDB_EXTRACT	data extraction
HKL-3000	data reduction
PHASER	phasing