4M9W | pdb_00004m9w

Crystal Structure of Ara h 8 with MES bound

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4M9B	PDB entry 4M9B

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	293	0.1 M MES (6.5), 25% PEG 2000MME, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.18	43.54

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 40.183	α = 90
b = 87.488	β = 95.84
c = 42.29	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	CCD	ADSC QUANTUM 315r		2012-06-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.98	APS	19-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	1.95	50	100	0.052	0.052	35.9	4.1	21429	21429		-3	33.4

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.95	1.98	99.6		0.364	0.364	2.9	3.9	1081

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	PDB entry 4M9B	1.95	40.01	20162	20162	1092	99.96	0.20758	0.20758	0.2054	0.2078	0.24796	0.2463	RANDOM	42.889

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]
2.98		-2.62	-4		1.26

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.802
r_dihedral_angle_4_deg	17.14
r_dihedral_angle_3_deg	14.659
r_dihedral_angle_1_deg	6.556
r_angle_refined_deg	1.781
r_angle_other_deg	1.234
r_chiral_restr	0.105
r_bond_refined_d	0.016
r_gen_planes_refined	0.009
r_gen_planes_other	0.006
r_bond_other_d	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2357
Nucleic Acid Atoms
Solvent Atoms	137
Heterogen Atoms	14

Software

Software
Software Name	Purpose
HKL-3000	data collection
HKL-3000	phasing
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling