2FKM | pdb_00002fkm

PMM/PGM S108D mutant with alpha-d-glucose 1,6-bisphosphate bound

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1P5D	pdb id 1P5D

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	298	50-60% sat Na K tartrate, .1 M Na Hepes pH 7.5 seeding used, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.07	40.68

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 70.222	α = 90
b = 70.356	β = 90
c = 84.392	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	NOIR-1		2005-03-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 4.2.2	0.97909	ALS	4.2.2

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	1.9	42.83	99.9	0.075	13.9	6.49	33627	33583

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)
1	1.9	1.97	99.4		0.346	4		3296

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	MOLECULAR REPLACEMENT	THROUGHOUT	pdb id 1P5D	1.9	42.83	33583	33583	1699	99.88	0.205	0.205	0.203	0.2066	0.251	0.2534	RANDOM	29.117

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]
-0.28			-1.18		1.46

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.175
r_dihedral_angle_4_deg	14.74
r_dihedral_angle_3_deg	13.107
r_dihedral_angle_1_deg	5.855
r_scangle_it	2.484
r_scbond_it	1.766
r_angle_refined_deg	1.225
r_angle_other_deg	0.761
r_mcangle_it	0.668
r_mcbond_it	0.552
r_nbd_refined	0.199
r_symmetry_vdw_other	0.194
r_symmetry_vdw_refined	0.184
r_symmetry_hbond_refined	0.178
r_nbd_other	0.177
r_nbtor_refined	0.176
r_xyhbond_nbd_refined	0.161
r_mcbond_other	0.109
r_nbtor_other	0.083
r_chiral_restr	0.069
r_metal_ion_refined	0.024
r_bond_refined_d	0.009
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3375
Nucleic Acid Atoms
Solvent Atoms	234
Heterogen Atoms	21

Software

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