7PB3

Structural and Functional analysis of the Proline Racemase (ProR) from the Gram-positive bacterium Acetoanaerobium sticklandii

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	291	1.26 M Ammonium Sulphate, 100 mM Cacodylate, pH 6.5 at rtp

Crystal Properties
Matthews coefficient	Solvent content
2.52	51

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 109.041	α = 90
b = 109.041	β = 90
c = 105.163	γ = 90

Symmetry
Space Group	P 43 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 PILATUS 6M-F		2018-09-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.91587	Diamond	I04-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.84	109.1	89.7	0.112	0.046	0.999	13.6	12.6		9545			109.1

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.84	3.29	68.2		1.877	0.769	0.584	1.5	12.3

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	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	6j7c	2.841	77.223	9530	542	61.432	0.256	0.2513	0.3296	126.233

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]
4.282			4.282		-8.564

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.879
r_dihedral_angle_3_deg	20.383
r_dihedral_angle_4_deg	13.501
r_dihedral_angle_1_deg	9.703
r_lrange_it	5.513
r_lrange_other	5.513
r_mcangle_it	2.996
r_mcangle_other	2.996
r_scangle_it	2.429
r_scangle_other	2.429
r_mcbond_it	1.741
r_mcbond_other	1.741
r_angle_refined_deg	1.429
r_scbond_it	1.32
r_scbond_other	1.32
r_angle_other_deg	1.058
r_nbd_refined	0.223
r_nbd_other	0.201
r_symmetry_nbd_other	0.195
r_xyhbond_nbd_refined	0.191
r_symmetry_xyhbond_nbd_refined	0.168
r_symmetry_nbd_refined	0.166
r_nbtor_refined	0.161
r_symmetry_xyhbond_nbd_other	0.097
r_symmetry_nbtor_other	0.073
r_chiral_restr	0.058
r_gen_planes_refined	0.004
r_bond_refined_d	0.003
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5172
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	16

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
STARANISO	data scaling
DIALS	data scaling
MoRDa	phasing
PHASER	phasing