9GID

NMDA bound to compound 338

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1PB9

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.7	282.15	20% (w/v) PEG 3350, 0.1 M Bis-Tris pH 5.7 and 0.2 M lithium sulfate

Crystal Properties
Matthews coefficient	Solvent content
2.19	43.92

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 41.56	α = 90
b = 72.5	β = 90
c = 95.79	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	RIGAKU SATURN 944		2017-01-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.54

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	23.96	95.1	0.171	0.974	4.3	2.4		45513

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2	2.05			0.729	0.478	0.8

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2	23.96	19090	993	94.379	0.209	0.2061	0.2598	RANDOM	23.026

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]
0.246			0.37		-0.616

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.124
r_dihedral_angle_3_deg	13.969
r_dihedral_angle_2_deg	7.899
r_dihedral_angle_1_deg	7.11
r_lrange_it	6.627
r_lrange_other	6.597
r_scangle_it	3.975
r_scangle_other	3.947
r_mcangle_it	3.387
r_mcangle_other	3.386
r_scbond_it	2.554
r_scbond_other	2.511
r_mcbond_it	2.164
r_mcbond_other	2.161
r_angle_refined_deg	1.628
r_angle_other_deg	0.535
r_symmetry_xyhbond_nbd_refined	0.238
r_nbd_other	0.228
r_nbd_refined	0.203
r_xyhbond_nbd_refined	0.192
r_symmetry_nbd_other	0.189
r_nbtor_refined	0.181
r_symmetry_nbd_refined	0.119
r_symmetry_nbtor_other	0.086
r_chiral_restr	0.072
r_bond_refined_d	0.008
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_symmetry_xyhbond_nbd_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2223
Nucleic Acid Atoms
Solvent Atoms	161
Heterogen Atoms	30

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
Aimless	data scaling
PHASER	phasing