2H9W | pdb_00002h9w

Green fluorescent protein ground states: the influence of a second protonation site near the chromophore

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2H6V	PDB ENTRY 2H6V

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	9	298	AS, Tris, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.2	42.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 51.886	α = 90
b = 62.933	β = 90
c = 71.035	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	298	CCD	MARRESEARCH		2006-03-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM30A	0.979469	ESRF	BM30A

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	1.82	47.106	97.2	0.066	0.066	8.2	6.3	20710	20710	2	2

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	1.82	1.92	97.2		0.387	0.387	1.9	3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2H6V	1.82	47.09	2	20710	20710	1072	96.33	0.16732	0.16632	0.18	0.18594	RANDOM	19.482

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]
-0.69			-0.14		0.83

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.932
r_dihedral_angle_3_deg	13.291
r_dihedral_angle_4_deg	11.754
r_dihedral_angle_1_deg	6.402
r_scangle_it	3.525
r_scbond_it	2.645
r_angle_refined_deg	1.578
r_mcangle_it	1.561
r_mcbond_it	1.428
r_angle_other_deg	1.385
r_symmetry_vdw_other	0.311
r_nbd_refined	0.276
r_mcbond_other	0.202
r_nbd_other	0.199
r_symmetry_hbond_refined	0.189
r_symmetry_vdw_refined	0.179
r_nbtor_refined	0.177
r_xyhbond_nbd_refined	0.116
r_nbtor_other	0.086
r_chiral_restr	0.085
r_bond_refined_d	0.011
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1912
Nucleic Acid Atoms
Solvent Atoms	109
Heterogen Atoms	10

Software

Software
Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
CCP4	model building
REFMAC	refinement
CCP4	data scaling
CCP4	phasing