6I34

Crystal structure of Neanderthal glycine decarboxylase (P-protein)

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	293	0.1 M HEPES pH 7, 6 % PEG3350, 10 mM DTT

Crystal Properties
Matthews coefficient	Solvent content
2.32	47

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 86.873	α = 90
b = 124.381	β = 98.57
c = 201.304	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 6M		2017-10-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID30B	0.98	ESRF	ID30B

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim 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	2.1	47.9	99.9	0.192	0.993	5.3	5.1		245944		1

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.1	2.2	100		0.64	1.2	5.2

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	6I33	2.1	47.9	233556	12259	99.8	0.218	0.216	0.243	RANDOM	36.11

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]
-1.86		1.66	0.85		0.48

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.464
r_dihedral_angle_4_deg	18.277
r_dihedral_angle_3_deg	13.541
r_dihedral_angle_1_deg	6.149
r_long_range_B_refined	6.12
r_long_range_B_other	6.113
r_scangle_other	3.817
r_scbond_it	2.551
r_scbond_other	2.551
r_mcangle_it	2.406
r_mcangle_other	2.406
r_angle_refined_deg	1.915
r_angle_other_deg	1.619
r_mcbond_it	1.609
r_mcbond_other	1.608
r_chiral_restr	0.131
r_bond_refined_d	0.019
r_gen_planes_other	0.009
r_gen_planes_refined	0.008
r_bond_other_d	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	29751
Nucleic Acid Atoms
Solvent Atoms	1359
Heterogen Atoms	169

Software

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