9GIE

NMDA bound to compound 315

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	7.5	282.15	24% PEG 3350 and 0.1 M hepes pH 7.5

Crystal Properties
Matthews coefficient	Solvent content
2.11	41.81

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 72.448	α = 90
b = 78.868	β = 90
c = 91.984	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	PIXEL	DECTRIS PILATUS3 6M		2016-01-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9763	Diamond	I03

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	2.36	91.98	100	0.143	1	12.8	6		22308

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	2.36	2.4			0.823	0.8	2.3

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	2.36	59.945	22258	1115	99.865	0.197	0.1941	0.2602	RANDOM	50.194

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]
0.734			-2.862		2.128

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.659
r_dihedral_angle_3_deg	14.162
r_lrange_other	10.687
r_lrange_it	10.684
r_scangle_it	7.285
r_scangle_other	7.284
r_dihedral_angle_1_deg	7.091
r_mcangle_it	6.838
r_mcangle_other	6.837
r_scbond_it	4.777
r_scbond_other	4.776
r_mcbond_it	4.577
r_mcbond_other	4.576
r_dihedral_angle_2_deg	3.659
r_angle_refined_deg	1.498
r_angle_other_deg	0.503
r_symmetry_nbd_refined	0.278
r_nbd_refined	0.181
r_nbd_other	0.17
r_nbtor_refined	0.169
r_symmetry_nbd_other	0.165
r_xyhbond_nbd_refined	0.165
r_symmetry_xyhbond_nbd_refined	0.127
r_symmetry_nbtor_other	0.079
r_chiral_restr	0.07
r_symmetry_xyhbond_nbd_other	0.027
r_bond_refined_d	0.007
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4191
Nucleic Acid Atoms
Solvent Atoms	55
Heterogen Atoms	52

Software

Software
Software Name	Purpose
REFMAC	refinement
autoPROC	data reduction
STARANISO	data scaling
PHASER	phasing