9GIC | pdb_00009gic

NMDA bound to compound 345

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
2.17	43.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 41.96	α = 90
b = 70.745	β = 90
c = 96	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	1.82	20.57	97.5	0.114	0.988	10.8	6		2553444

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	1.82	1.86			0.324	0.91	3.7

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.823	20.566	25480	1232	97.2	0.192	0.1906	0.1908	0.2205	0.2215	RANDOM	18.496

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]
-0.817			0.691		0.126

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.43
r_dihedral_angle_2_deg	13.49
r_dihedral_angle_3_deg	12.505
r_dihedral_angle_1_deg	6.763
r_lrange_it	6.338
r_lrange_other	6.295
r_scangle_it	4.186
r_scangle_other	4.158
r_mcangle_it	2.923
r_mcangle_other	2.923
r_scbond_it	2.665
r_scbond_other	2.606
r_mcbond_it	1.847
r_mcbond_other	1.847
r_angle_refined_deg	1.656
r_angle_other_deg	0.575
r_symmetry_nbd_refined	0.249
r_nbd_refined	0.208
r_nbd_other	0.201
r_symmetry_xyhbond_nbd_refined	0.191
r_symmetry_nbd_other	0.182
r_nbtor_refined	0.18
r_xyhbond_nbd_refined	0.126
r_symmetry_nbtor_other	0.087
r_chiral_restr	0.082
r_symmetry_xyhbond_nbd_other	0.013
r_bond_refined_d	0.009
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2227
Nucleic Acid Atoms
Solvent Atoms	171
Heterogen Atoms	31

Software

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