2QMS | pdb_00002qms

Crystal structure of a signaling molecule

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.1	295	0.1M sodium citrate pH6.1, 22.5% PEG 4000, 0.2M Ammonium sulphate, 5 % glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
1.93	36.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 62.649	α = 90
b = 63.904	β = 90
c = 105.685	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	IMAGE PLATE	MAR scanner 345 mm plate	osmic mirrors	2004-01-01		SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RUH2R	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	44.7	99.1	0.084	12.6	3.1		25401			28.4

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.1	2.15	99.4		0.505	2.2		1269

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 (Observed)	R-Work (Depositor)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.1	30	25218	1269	99.18	0.203	0.201	0.255	0.2367	RANDOM	37.848

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]
-0.63			-0.54		1.17

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.359
r_dihedral_angle_4_deg	17.822
r_dihedral_angle_3_deg	15.359
r_dihedral_angle_1_deg	6.793
r_mcangle_it	2.771
r_scangle_it	2.61
r_mcbond_it	1.776
r_scbond_it	1.772
r_angle_refined_deg	1.486
r_nbtor_refined	0.302
r_symmetry_vdw_refined	0.227
r_nbd_refined	0.202
r_xyhbond_nbd_refined	0.144
r_symmetry_hbond_refined	0.128
r_chiral_restr	0.094
r_bond_refined_d	0.014
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3733
Nucleic Acid Atoms
Solvent Atoms	181
Heterogen Atoms	35

Software

Software
Software Name	Purpose
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
d*TREK	data scaling
DENZO	data reduction
SCALEPACK	data scaling